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Ekeberg T, Assalauova D, Bielecki J, Boll R, Daurer BJ, Eichacker LA, Franken LE, Galli DE, Gelisio L, Gumprecht L, Gunn LH, Hajdu J, Hartmann R, Hasse D, Ignatenko A, Koliyadu J, Kulyk O, Kurta R, Kuster M, Lugmayr W, Lübke J, Mancuso AP, Mazza T, Nettelblad C, Ovcharenko Y, Rivas DE, Rose M, Samanta AK, Schmidt P, Sobolev E, Timneanu N, Usenko S, Westphal D, Wollweber T, Worbs L, Xavier PL, Yousef H, Ayyer K, Chapman HN, Sellberg JA, Seuring C, Vartanyants IA, Küpper J, Meyer M, Maia FRNC. Observation of a single protein by ultrafast X-ray diffraction. Light Sci Appl 2024; 13:15. [PMID: 38216563 PMCID: PMC10786860 DOI: 10.1038/s41377-023-01352-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/14/2024]
Abstract
The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.
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Affiliation(s)
- Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Dameli Assalauova
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Rebecca Boll
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Benedikt J Daurer
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK
| | - Lutz A Eichacker
- University of Stavanger, Centre Organelle Research, Richard-Johnsensgate 4, 4021, Stavanger, Norway
| | - Linda E Franken
- Leibniz Institute for Experimental Virology (HPI), Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany
| | - Davide E Galli
- Dipartimento di Fisica "Aldo Pontremoli", Università degli Studi di Milano, via Celoria 16, 20133, Milano, Italy
| | - Luca Gelisio
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Lars Gumprecht
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
| | - Laura H Gunn
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | | | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Alexandr Ignatenko
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jayanath Koliyadu
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-10691, Stockholm, Sweden
| | - Olena Kulyk
- ELI Beamlines/IoP Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Ruslan Kurta
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Markus Kuster
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Wolfgang Lugmayr
- Multi-User CryoEM Facility, Centre for Structural Systems Biology, Notkestr.85, 22607, Hamburg, Germany
- University Medical Center Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246, Hamburg, Germany
| | - Jannik Lübke
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Tommaso Mazza
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Carl Nettelblad
- Division of Scientific Computing, Science for Life Laboratory, Department of Information Technology, Uppsala University, Box 337, SE-75105, Uppsala, Sweden
| | | | | | - Max Rose
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Amit K Samanta
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
| | | | - Egor Sobolev
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala, Sweden
| | - Sergey Usenko
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Tamme Wollweber
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Lena Worbs
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Paul Lourdu Xavier
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Hazem Yousef
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Kartik Ayyer
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Jonas A Sellberg
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-10691, Stockholm, Sweden
| | - Carolin Seuring
- Multi-User CryoEM Facility, Centre for Structural Systems Biology, Notkestr.85, 22607, Hamburg, Germany
- Department of Chemistry, Universität Hamburg, 20146, Hamburg, Germany
| | - Ivan A Vartanyants
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jochen Küpper
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Michael Meyer
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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2
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Pilipenco A, Forinová M, Mašková H, Hönig V, Palus M, Lynn Jr. NS, Víšová I, Vrabcová M, Houska M, Anthi J, Spasovová M, Mustacová J, Štěrba J, Dostálek J, Tung CP, Yang AS, Jack R, Dejneka A, Hajdu J, Vaisocherová-Lísalová H. Negligible risk of surface transmission of SARS-CoV-2 in public transportation. J Travel Med 2023; 30:taad065. [PMID: 37133444 PMCID: PMC10481417 DOI: 10.1093/jtm/taad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/14/2023] [Accepted: 04/22/2023] [Indexed: 05/04/2023]
Abstract
BACKGROUND Exposure to pathogens in public transport systems is a common means of spreading infection, mainly by inhaling aerosol or droplets from infected individuals. Such particles also contaminate surfaces, creating a potential surface-transmission pathway. METHODS A fast acoustic biosensor with an antifouling nano-coating was introduced to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on exposed surfaces in the Prague Public Transport System. Samples were measured directly without pre-treatment. Results with the sensor gave excellent agreement with parallel quantitative reverse-transcription polymerase chain reaction (qRT-PCR) measurements on 482 surface samples taken from actively used trams, buses, metro trains and platforms between 7 and 9 April 2021, in the middle of the lineage Alpha SARS-CoV-2 epidemic wave when 1 in 240 people were COVID-19 positive in Prague. RESULTS Only ten of the 482 surface swabs produced positive results and none of them contained virus particles capable of replication, indicating that positive samples contained inactive virus particles and/or fragments. Measurements of the rate of decay of SARS-CoV-2 on frequently touched surface materials showed that the virus did not remain viable longer than 1-4 h. The rate of inactivation was the fastest on rubber handrails in metro escalators and the slowest on hard-plastic seats, window glasses and stainless-steel grab rails. As a result of this study, Prague Public Transport Systems revised their cleaning protocols and the lengths of parking times during the pandemic. CONCLUSIONS Our findings suggest that surface transmission played no or negligible role in spreading SARS-CoV-2 in Prague. The results also demonstrate the potential of the new biosensor to serve as a complementary screening tool in epidemic monitoring and prognosis.
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Affiliation(s)
- Alina Pilipenco
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Michala Forinová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Hana Mašková
- Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 370 05 České Budějovice, Czech Republic
| | - Václav Hönig
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic
| | - Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic
| | - Nicholas Scott Lynn Jr.
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Ivana Víšová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Markéta Vrabcová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Milan Houska
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Judita Anthi
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Monika Spasovová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Johana Mustacová
- Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 370 05 České Budějovice, Czech Republic
| | - Ján Štěrba
- Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 370 05 České Budějovice, Czech Republic
| | - Jakub Dostálek
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Chao-Ping Tung
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Rachael Jack
- The European Extreme Light Infrastructure, ERIC, Za Radnici 835, 25241 Dolní Břežany, Czech Republic
| | - Alexandr Dejneka
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Janos Hajdu
- The European Extreme Light Infrastructure, ERIC, Za Radnici 835, 25241 Dolní Břežany, Czech Republic
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 751 24 Uppsala, Sweden
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3
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Assalauova D, Kim YY, Bobkov S, Khubbutdinov R, Rose M, Alvarez R, Andreasson J, Balaur E, Contreras A, DeMirci H, Gelisio L, Hajdu J, Hunter MS, Kurta RP, Li H, McFadden M, Nazari R, Schwander P, Teslyuk A, Walter P, Xavier PL, Yoon CH, Zaare S, Ilyin VA, Kirian RA, Hogue BG, Aquila A, Vartanyants IA. Erratum: An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. Corrigendum. IUCrJ 2022; 9:328. [PMID: 35371497 PMCID: PMC8895016 DOI: 10.1107/s2052252522000501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
[This corrects the article DOI: 10.1107/S2052252520012798.].
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Affiliation(s)
- Dameli Assalauova
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Young Yong Kim
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Sergey Bobkov
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
| | - Ruslan Khubbutdinov
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe sh. 31, Moscow, 115409, Russian Federation
| | - Max Rose
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Roberto Alvarez
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- School of Mathematics and Statistical Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Jakob Andreasson
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic
| | - Eugeniu Balaur
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria 3086, Australia
| | - Alice Contreras
- School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Hasan DeMirci
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Molecular Biology and Genetics, Koc University, Istanbul, 34450, Turkey
| | - Luca Gelisio
- Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Janos Hajdu
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, SE-75124, Sweden
| | - Mark S. Hunter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | | | - Haoyuan Li
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Physics Department, Stanford University, 450 Jane Stanford Way, Stanford, CA 94305-2004, USA
| | - Matthew McFadden
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Reza Nazari
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | | | - Anton Teslyuk
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
- Moscow Institute of Physics and Technology, Moscow, 141700, Russian Federation
| | - Peter Walter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - P. Lourdu Xavier
- Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, D-22761, Germany
| | - Chun Hong Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sahba Zaare
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Viacheslav A. Ilyin
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
- Moscow Institute of Physics and Technology, Moscow, 141700, Russian Federation
| | - Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Brenda G. Hogue
- School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ivan A. Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe sh. 31, Moscow, 115409, Russian Federation
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4
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Han H, Round E, Schubert R, Gül Y, Makroczyová J, Meza D, Heuser P, Aepfelbacher M, Barák I, Betzel C, Fromme P, Kursula I, Nissen P, Tereschenko E, Schulz J, Uetrecht C, Ulicný J, Wilmanns M, Hajdu J, Lamzin VS, Lorenzen K. The XBI BioLab for life science experiments at the European XFEL. J Appl Crystallogr 2021; 54:7-21. [PMID: 33833637 PMCID: PMC7941304 DOI: 10.1107/s1600576720013989] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/19/2020] [Indexed: 11/26/2022] Open
Abstract
The science of X-ray free-electron lasers (XFELs) critically depends on the performance of the X-ray laser and on the quality of the samples placed into the X-ray beam. The stability of biological samples is limited and key biomolecular transformations occur on short timescales. Experiments in biology require a support laboratory in the immediate vicinity of the beamlines. The XBI BioLab of the European XFEL (XBI denotes XFEL Biology Infrastructure) is an integrated user facility connected to the beamlines for supporting a wide range of biological experiments. The laboratory was financed and built by a collaboration between the European XFEL and the XBI User Consortium, whose members come from Finland, Germany, the Slovak Republic, Sweden and the USA, with observers from Denmark and the Russian Federation. Arranged around a central wet laboratory, the XBI BioLab provides facilities for sample preparation and scoring, laboratories for growing prokaryotic and eukaryotic cells, a Bio Safety Level 2 laboratory, sample purification and characterization facilities, a crystallization laboratory, an anaerobic laboratory, an aerosol laboratory, a vacuum laboratory for injector tests, and laboratories for optical microscopy, atomic force microscopy and electron microscopy. Here, an overview of the XBI facility is given and some of the results of the first user experiments are highlighted.
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Affiliation(s)
- Huijong Han
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Ekaterina Round
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Yasmin Gül
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jana Makroczyová
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovak Republic
| | - Domingo Meza
- Biodesign Center for Applied Structural Discovery and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Philipp Heuser
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Imrich Barák
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovak Republic
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Inari Kursula
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Poul Nissen
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK – 8000 Aarhus C, Denmark
| | - Elena Tereschenko
- Institute of Crystallography, Russian Academy of Sciences, 59 Leninsky prospekt, Moscow, 117333, Russian Federation
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Charlotte Uetrecht
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Jozef Ulicný
- Department of Biophysics, Institute of Physics, Faculty of Science, P. J. Šafárik University, Jesenná 5, 04154 Košice, Slovak Republic
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Janos Hajdu
- The European Extreme Light Infrastructure, Institute of Physics, Academy of Sciences of the Czech Republic, Za Radnici 835, 25241 Dolní Břežany, Czech Republic
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Victor S. Lamzin
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
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5
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Li H, Nazari R, Abbey B, Alvarez R, Aquila A, Ayyer K, Barty A, Berntsen P, Bielecki J, Pietrini A, Bucher M, Carini G, Chapman HN, Contreras A, Daurer BJ, DeMirci H, Flűckiger L, Frank M, Hajdu J, Hantke MF, Hogue BG, Hosseinizadeh A, Hunter MS, Jönsson HO, Kirian RA, Kurta RP, Loh D, Maia FRNC, Mancuso AP, Morgan AJ, McFadden M, Muehlig K, Munke A, Reddy HKN, Nettelblad C, Ourmazd A, Rose M, Schwander P, Marvin Seibert M, Sellberg JA, Sierra RG, Sun Z, Svenda M, Vartanyants IA, Walter P, Westphal D, Williams G, Xavier PL, Yoon CH, Zaare S. Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source. Sci Data 2020; 7:404. [PMID: 33214568 PMCID: PMC7678860 DOI: 10.1038/s41597-020-00745-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/29/2020] [Indexed: 11/18/2022] Open
Abstract
Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.
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Affiliation(s)
- Haoyuan Li
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
- Physics Department, Stanford University, 450 Serra Mall, Stanford, California, 94305, USA
| | - Reza Nazari
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Brian Abbey
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Roberto Alvarez
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA.
| | - Kartik Ayyer
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Anton Barty
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- DESY, Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - Peter Berntsen
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Johan Bielecki
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Alberto Pietrini
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Maximilian Bucher
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Gabriella Carini
- Brookhaven National Laboratory, Bldg 535B, Upton, NY, 11973, USA
| | - Henry N Chapman
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Alice Contreras
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Benedikt J Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - Hasan DeMirci
- Stanford PULSE Institute, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
- Koc University, Rumelifeneri, Sariyer Rumeli Feneri Yolu, 34450, Sariyer/Istanbul, Turkey
| | - Leonie Flűckiger
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, L-452, Livermore, California, 94550, USA
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
- The European Extreme Light Infrastructure, Institute of Physics, Academy of Sciences of the Czech Republic, Za Radnicic 835, 25241, Dolní Břežany, Czech Republic
| | - Max F Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Brenda G Hogue
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Ahmad Hosseinizadeh
- University of Wisconsin Milwaukee, 3135N. Maryland Ave, Milwaukee, Wisconsin, 53211, USA
| | - Mark S Hunter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - H Olof Jönsson
- Department of Applied Physics, KTH Royal Institute of Technology, AlbaNova University Center, KTH Royal Institute of Technology, S-106 91, Stockholm, Sweden
| | - Richard A Kirian
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | | | - Duane Loh
- Department of Physics, National University of Singapore, 14 Science Drive 4, Blk S1A, Level 2, S1A-02-07, Lee Wee Kheng Building, Singapore, 117557, Singapore
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Andrew J Morgan
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Matthew McFadden
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Kerstin Muehlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Anna Munke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Hemanth Kumar Narayana Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Abbas Ourmazd
- University of Wisconsin Milwaukee, 3135N. Maryland Ave, Milwaukee, Wisconsin, 53211, USA
| | - Max Rose
- DESY, Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - Peter Schwander
- University of Wisconsin Milwaukee, 3135N. Maryland Ave, Milwaukee, Wisconsin, 53211, USA
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Jonas A Sellberg
- Department of Applied Physics, KTH Royal Institute of Technology, AlbaNova University Center, KTH Royal Institute of Technology, S-106 91, Stockholm, Sweden
| | - Raymond G Sierra
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Zhibin Sun
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
- Photon Science Division, Paul Scherrer Institute, CH-5232, Villigen PSI, Switzerland
| | - Martin Svenda
- Department of Applied Physics, KTH Royal Institute of Technology, AlbaNova University Center, KTH Royal Institute of Technology, S-106 91, Stockholm, Sweden
| | - Ivan A Vartanyants
- DESY, Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
- NRNU MEPhI, Kashirskoe shosse 31, 115409, Moscow, Russia
| | - Peter Walter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Garth Williams
- Brookhaven National Laboratory, Bldg 535B, Upton, NY, 11973, USA
| | - P Lourdu Xavier
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Chun Hong Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Sahba Zaare
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
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6
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Assalauova D, Kim YY, Bobkov S, Khubbutdinov R, Rose M, Alvarez R, Andreasson J, Balaur E, Contreras A, DeMirci H, Gelisio L, Hajdu J, Hunter MS, Kurta RP, Li H, McFadden M, Nazari R, Schwander P, Teslyuk A, Walter P, Xavier PL, Yoon CH, Zaare S, Ilyin VA, Kirian RA, Hogue BG, Aquila A, Vartanyants IA. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. IUCrJ 2020; 7:1102-1113. [PMID: 33209321 PMCID: PMC7642788 DOI: 10.1107/s2052252520012798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/21/2020] [Indexed: 05/06/2023]
Abstract
An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.
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Affiliation(s)
- Dameli Assalauova
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Young Yong Kim
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Sergey Bobkov
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
| | - Ruslan Khubbutdinov
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe sh. 31, Moscow, 115409, Russian Federation
| | - Max Rose
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Roberto Alvarez
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- School of Mathematics and Statistical Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Jakob Andreasson
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic
| | - Eugeniu Balaur
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria 3086, Australia
| | - Alice Contreras
- School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Hasan DeMirci
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Molecular Biology and Genetics, Koc University, Istanbul, 34450, Turkey
| | - Luca Gelisio
- Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Janos Hajdu
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, SE-75124, Sweden
| | - Mark S. Hunter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | | | - Haoyuan Li
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Physics Department, Stanford University, 450 Jane Stanford Way, Stanford, CA 94305-2004, USA
| | - Matthew McFadden
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Reza Nazari
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | | | - Anton Teslyuk
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
- Moscow Institute of Physics and Technology, Moscow, 141700, Russian Federation
| | - Peter Walter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - P. Lourdu Xavier
- Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, D-22761, Germany
| | - Chun Hong Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sahba Zaare
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Viacheslav A. Ilyin
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
- Moscow Institute of Physics and Technology, Moscow, 141700, Russian Federation
| | - Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Brenda G. Hogue
- School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ivan A. Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe sh. 31, Moscow, 115409, Russian Federation
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7
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Polovinkin V, Khakurel K, Babiak M, Angelov B, Schneider B, Dohnalek J, Andreasson J, Hajdu J. Demonstration of electron diffraction from membrane protein crystals grown in a lipidic mesophase after lamella preparation by focused ion beam milling at cryogenic temperatures. J Appl Crystallogr 2020; 53:1416-1424. [PMID: 33304220 PMCID: PMC7710488 DOI: 10.1107/s1600576720013096] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/27/2020] [Indexed: 12/26/2022] Open
Abstract
Electron diffraction experiments on crystals of membrane proteins grown in lipidic mesophases have not been possible owing to a thick layer of viscous crystallization medium around the crystals. Here it is shown that focused ion beam milling at cryogenic temperatures (cryo-FIB milling) can remove the viscous layer, and high-quality electron diffraction on a FIB-milled lamella of a bacteriorhodopsin 3D crystal is demonstrated. Electron crystallography of sub-micrometre-sized 3D protein crystals has emerged recently as a valuable field of structural biology. In meso crystallization methods, utilizing lipidic mesophases, particularly lipidic cubic phases (LCPs), can produce high-quality 3D crystals of membrane proteins (MPs). A major step towards realizing 3D electron crystallography of MP crystals, grown in meso, is to demonstrate electron diffraction from such crystals. The first task is to remove the viscous and sticky lipidic matrix that surrounds the crystals without damaging the crystals. Additionally, the crystals have to be thin enough to let electrons traverse them without significant multiple scattering. In the present work, the concept that focused ion beam milling at cryogenic temperatures (cryo-FIB milling) can be used to remove excess host lipidic mesophase matrix is experimentally verified, and then the crystals are thinned to a thickness suitable for electron diffraction. In this study, bacteriorhodopsin (BR) crystals grown in a lipidic cubic mesophase of monoolein were used as a model system. LCP from a part of a hexagon-shaped plate-like BR crystal (∼10 µm in thickness and ∼70 µm in the longest dimension), which was flash-frozen in liquid nitrogen, was milled away with a gallium FIB under cryogenic conditions, and a part of the crystal itself was thinned into a ∼210 nm-thick lamella with the ion beam. The frozen sample was then transferred into an electron cryo-microscope, and a nanovolume of ∼1400 × 1400 × 210 nm of the BR lamella was exposed to 200 kV electrons at a fluence of ∼0.06 e Å−2. The resulting electron diffraction peaks were detected beyond 2.7 Å resolution (with an average peak height to background ratio of >2) by a CMOS-based Ceta 16M camera. The results demonstrate that cryo-FIB milling produces high-quality lamellae from crystals grown in lipidic mesophases and pave the way for 3D electron crystallography on crystals grown or embedded in highly viscous media.
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Affiliation(s)
- Vitaly Polovinkin
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic
| | - Krishna Khakurel
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic
| | - Michal Babiak
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/4, 62500 Brno, Czech Republic
| | - Borislav Angelov
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
| | - Jan Dohnalek
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
| | - Jakob Andreasson
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic
| | - Janos Hajdu
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 18221 Prague, Czech Republic.,Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
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8
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Vinko SM, Vozda V, Andreasson J, Bajt S, Bielecki J, Burian T, Chalupsky J, Ciricosta O, Desjarlais MP, Fleckenstein H, Hajdu J, Hajkova V, Hollebon P, Juha L, Kasim MF, McBride EE, Muehlig K, Preston TR, Rackstraw DS, Roling S, Toleikis S, Wark JS, Zacharias H. Time-Resolved XUV Opacity Measurements of Warm Dense Aluminum. Phys Rev Lett 2020; 124:225002. [PMID: 32567902 DOI: 10.1103/physrevlett.124.225002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 05/02/2020] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
The free-free opacity in plasmas is fundamental to our understanding of energy transport in stellar interiors and for inertial confinement fusion research. However, theoretical predictions in the challenging dense plasma regime are conflicting and there is a dearth of accurate experimental data to allow for direct model validation. Here we present time-resolved transmission measurements in solid-density Al heated by an XUV free-electron laser. We use a novel functional optimization approach to extract the temperature-dependent absorption coefficient directly from an oversampled pool of single-shot measurements, and find a pronounced enhancement of the opacity as the plasma is heated to temperatures of order of the Fermi energy. Plasma heating and opacity enhancement are observed on ultrafast timescales, within the duration of the femtosecond XUV pulse. We attribute further rises in the opacity on ps timescales to melt and the formation of warm dense matter.
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Affiliation(s)
- S M Vinko
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - V Vozda
- Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 18221 Prague 8, Czech Republic
| | - J Andreasson
- ELI Beamlines, Institute of Physics, Czech Academy of Sciences, Na Slovance 2, CZ-182 21 Prague 8, Czech Republic
- Chalmers University of Technology, Department of Physics, 41296 Göteborg, Sweden
| | - S Bajt
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - J Bielecki
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - T Burian
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 18221 Prague 8, Czech Republic
| | - J Chalupsky
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 18221 Prague 8, Czech Republic
| | - O Ciricosta
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - M P Desjarlais
- Pulsed Power Sciences Center, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - H Fleckenstein
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - J Hajdu
- ELI Beamlines, Institute of Physics, Czech Academy of Sciences, Na Slovance 2, CZ-182 21 Prague 8, Czech Republic
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - V Hajkova
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 18221 Prague 8, Czech Republic
| | - P Hollebon
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - L Juha
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 18221 Prague 8, Czech Republic
| | - M F Kasim
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - E E McBride
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - K Muehlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596SE-751 24 Uppsala, Sweden
| | - T R Preston
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - D S Rackstraw
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - S Roling
- Universität Münster, Busso-Peus-Strasse 10, 48149 Münster, Germany
| | - S Toleikis
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - J S Wark
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - H Zacharias
- Universität Münster, Busso-Peus-Strasse 10, 48149 Münster, Germany
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9
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Andrikopoulos PC, Liu Y, Picchiotti A, Lenngren N, Kloz M, Chaudhari AS, Precek M, Rebarz M, Andreasson J, Hajdu J, Schneider B, Fuertes G. Femtosecond-to-nanosecond dynamics of flavin mononucleotide monitored by stimulated Raman spectroscopy and simulations. Phys Chem Chem Phys 2020; 22:6538-6552. [PMID: 31994556 DOI: 10.1039/c9cp04918e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Flavin mononucleotide (FMN) belongs to the large family of flavins, ubiquitous yellow-coloured biological chromophores that contain an isoalloxazine ring system. As a cofactor in flavoproteins, it is found in various enzymes and photosensory receptors, like those featuring the light-oxygen-voltage (LOV) domain. The photocycle of FMN is triggered by blue light and proceeds via a cascade of intermediate states. In this work, we have studied isolated FMN in an aqueous solution in order to elucidate the intrinsic electronic and vibrational changes of the chromophore upon excitation. The ultrafast transitions of excited FMN were monitored through the joint use of femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption spectroscopy encompassing a time window between 0 ps and 6 ns with 50 fs time resolution. Global analysis of the obtained transient visible absorption and transient Raman spectra in combination with extensive quantum chemistry calculations identified unambiguously the singlet and triplet FMN populations and addressed solvent dynamics effects. The good agreement between the experimental and theoretical spectra facilitated the assignment of electronic transitions and vibrations. Our results represent the first steps towards more complex experiments aimed at tracking structural changes of FMN embedded in light-inducible proteins upon photoexcitation.
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Affiliation(s)
- Prokopis C Andrikopoulos
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czech Republic.
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10
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Ho PJ, Daurer BJ, Hantke MF, Bielecki J, Al Haddad A, Bucher M, Doumy G, Ferguson KR, Flückiger L, Gorkhover T, Iwan B, Knight C, Moeller S, Osipov T, Ray D, Southworth SH, Svenda M, Timneanu N, Ulmer A, Walter P, Hajdu J, Young L, Maia FRNC, Bostedt C. The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters. Nat Commun 2020; 11:167. [PMID: 31919346 PMCID: PMC6952381 DOI: 10.1038/s41467-019-13905-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/04/2019] [Indexed: 11/09/2022] Open
Abstract
Intense x-ray free-electron laser (XFEL) pulses hold great promise for imaging function in nanoscale and biological systems with atomic resolution. So far, however, the spatial resolution obtained from single shot experiments lags averaging static experiments. Here we report on a combined computational and experimental study about ultrafast diffractive imaging of sucrose clusters which are benchmark organic samples. Our theoretical model matches the experimental data from the water window to the keV x-ray regime. The large-scale dynamic scattering calculations reveal that transient phenomena driven by non-linear x-ray interaction are decisive for ultrafast imaging applications. Our study illuminates the complex interplay of the imaging process with the rapidly changing transient electronic structures in XFEL experiments and shows how computational models allow optimization of the parameters for ultrafast imaging experiments. X-ray free electron lasers provide high photon flux to explore single particle diffraction imaging of biological samples. Here the authors present dynamic electronic structure calculations and benchmark them to single-particle XFEL diffraction data of sucrose clusters to predict optimal single-shot imaging conditions.
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Affiliation(s)
- Phay J Ho
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
| | - Benedikt J Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Max F Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.,Chemistry Research Laboratory, Department of Chemistry, Oxford University, 12 Mansfield Rd, Oxford, OX1 3TA, UK
| | - Johan Bielecki
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.,European XFEL GmbH, Holzkoppel 4, D-22869, Schenefeld, Germany
| | - Andre Al Haddad
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Maximilian Bucher
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Gilles Doumy
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Ken R Ferguson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Leonie Flückiger
- ARC Centre of Excellence for Advanced Molecular Imaging, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Tais Gorkhover
- Stanford Pulse Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Bianca Iwan
- Stanford Pulse Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Christopher Knight
- Computational Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Stefan Moeller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Timur Osipov
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Dipanwita Ray
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Stephen H Southworth
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.,Department of Physics and Astronomy, Uppsala University, SE-751 20, Uppsala, Sweden
| | - Anatoli Ulmer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623, Berlin, Germany
| | - Peter Walter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Linda Young
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA.,Department of Physics and James Franck Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.
| | - Christoph Bostedt
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA. .,Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA. .,Paul-Scherrer Institute, CH-5232, Villigen PSI, Switzerland. .,LUXS Laboratory for Ultrafast X-ray Sciences, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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11
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Reddy HK, Carroni M, Hajdu J, Svenda M. Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture. eLife 2019; 8:48496. [PMID: 31513011 PMCID: PMC6750898 DOI: 10.7554/elife.48496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022] Open
Abstract
Bacteriophage PR772, a member of the Tectiviridae family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 Å, while the resolution of the protein capsid is 2.3 Å. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T = 25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.
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Affiliation(s)
- Hemanth Kn Reddy
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Uppsala, Sweden
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Janos Hajdu
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Uppsala, Sweden.,Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Martin Svenda
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Uppsala, Sweden.,Department of Applied Physics, Biomedical and X-Ray Physics, KTH Royal Institute of Technology, Stockholm, Sweden
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12
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Mühlig K, Gañán-Calvo AM, Andreasson J, Larsson DSD, Hajdu J, Svenda M. Nanometre-sized droplets from a gas dynamic virtual nozzle. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719008318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
This paper reports on improved techniques to create and characterize nanometre-sized droplets from dilute aqueous solutions by using a gas dynamic virtual nozzle (GDVN). It describes a method to measure the size distribution of uncharged droplets, using an environmental scanning electron microscope, and provides theoretical models for the droplet sizes created. The results show that droplet sizes can be tuned by adjusting the gas and liquid flow rates in the GDVN, and at the lowest liquid flow rates, the size of the water droplets peaks at about 120 nm. This droplet size is similar to droplet sizes produced by electrospray ionization but requires neither electrolytes nor charging of the solution. The results presented here identify a new operational regime for GDVNs and show that predictable droplet sizes, comparable to those obtained by electrospray ionization, can be produced by purely mechanical means in GDVNs.
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13
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Klimešová E, Kulyk O, Gu Y, Dittrich L, Korn G, Hajdu J, Krikunova M, Andreasson J. Plasma channel formation in NIR laser-irradiated carrier gas from an aerosol nanoparticle injector. Sci Rep 2019; 9:8851. [PMID: 31221980 PMCID: PMC6586673 DOI: 10.1038/s41598-019-45120-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/22/2019] [Indexed: 11/30/2022] Open
Abstract
Aerosol nanoparticle injectors are fundamentally important for experiments where container-free sample handling is needed to study isolated nanoparticles. The injector consists of a nebuliser, a differential pumping unit, and an aerodynamic lens to create and deliver a focused particle beam to the interaction point inside a vacuum chamber. The tightest focus of the particle beam is close to the injector tip. The density of the focusing carrier gas is high at this point. We show here how this gas interacts with a near infrared laser pulse (800 nm wavelength, 120 fs pulse duration) at intensities approaching 1016 Wcm-2. We observe acceleration of gas ions to kinetic energies of 100s eV and study their energies as a function of the carrier gas density. Our results indicate that field ionisation by the intense near-infrared laser pulse opens up a plasma channel behind the laser pulse. The observations can be understood in terms of a Coulomb explosion of the created underdense plasma channel. The results can be used to estimate gas background in experiments with the injector and they open up opportunities for a new class of studies on electron and ion dynamics in nanoparticles surrounded by a low-density gas.
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Affiliation(s)
- Eva Klimešová
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic.
| | - Olena Kulyk
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Yanjun Gu
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Laura Dittrich
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
- Technische Universität Berlin, Institut für Optik und Atomare Physik, ER 1-1, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Georg Korn
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Janos Hajdu
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Maria Krikunova
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
- Technische Universität Berlin, Institut für Optik und Atomare Physik, ER 1-1, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Jakob Andreasson
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
- Chalmers University of Technology, Department of Physics, Göteborg, Sweden
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14
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Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN. Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. IUCrJ 2019; 6:341-343. [PMID: 31098014 PMCID: PMC6503929 DOI: 10.1107/s2052252519005918] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The policy of IUCr Journals on diffraction data is defined.
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Affiliation(s)
- John R Helliwell
- School of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, United Kingdom
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908-0736, USA
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Randy J Read
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Mark J van Raaij
- CSIC, Centro Nacional de Biotecnologia, c/Darwin 3, Madrid, 28049, Spain
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden
- The European Extreme Light Infrastructure, Institute of Physics, AS CR, Na Slovance 2, Prague 18221 8, Czech Republic
| | - Edward N Baker
- School of Biological Sciences, University of Auckland, School of Biological Sciences, Private Bag 92-019, Auckland, New Zealand
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15
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Daurer BJ, Okamoto K, Bielecki J, Maia FRNC, Mühlig K, Seibert MM, Hantke MF, Nettelblad C, Benner WH, Svenda M, Tîmneanu N, Ekeberg T, Loh ND, Pietrini A, Zani A, Rath AD, Westphal D, Kirian RA, Awel S, Wiedorn MO, van der Schot G, Carlsson GH, Hasse D, Sellberg JA, Barty A, Andreasson J, Boutet S, Williams G, Koglin J, Andersson I, Hajdu J, Larsson DSD. Erratum: Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses. Corrigendum. IUCrJ 2019; 6:500. [PMID: 31098030 PMCID: PMC6503930 DOI: 10.1107/s2052252519004317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
[This corrects the article DOI: 10.1107/S2052252517003591.].
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Affiliation(s)
- Benedikt J. Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Kenta Okamoto
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Johan Bielecki
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kerstin Mühlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - M. Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Max F. Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Carl Nettelblad
- Division of Scientific Computing, Department of Information Technology, Science for Life Laboratory, Uppsala University, Lägerhyddsvägen 2 (Box 337), SE-751 05 Uppsala, Sweden
| | - W. Henry Benner
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Nicuşor Tîmneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Molecular and Condensed Matter Physics, Department of Physics and Astronomy, Uppsala University, Lägerhyddsvägen 1 (Box 516), SE-751 20 Uppsala, Sweden
| | - Tomas Ekeberg
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - N. Duane Loh
- Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Alberto Pietrini
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Alessandro Zani
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Asawari D. Rath
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Bhabha Atomic Research Center, Mumbai 400 085, India
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Richard A. Kirian
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Salah Awel
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Gunilla H. Carlsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Jonas A. Sellberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Garth Williams
- Brookhaven National Laboratory, 743 Brookhaven Avenue, Upton, NY 11973, USA
| | - Jason Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21 Prague 8, Czech Republic
| | - Daniel S. D. Larsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
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16
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Bielecki J, Hantke MF, Daurer BJ, Reddy HKN, Hasse D, Larsson DSD, Gunn LH, Svenda M, Munke A, Sellberg JA, Flueckiger L, Pietrini A, Nettelblad C, Lundholm I, Carlsson G, Okamoto K, Timneanu N, Westphal D, Kulyk O, Higashiura A, van der Schot G, Loh NTD, Wysong TE, Bostedt C, Gorkhover T, Iwan B, Seibert MM, Osipov T, Walter P, Hart P, Bucher M, Ulmer A, Ray D, Carini G, Ferguson KR, Andersson I, Andreasson J, Hajdu J, Maia FRNC. Electrospray sample injection for single-particle imaging with x-ray lasers. Sci Adv 2019; 5:eaav8801. [PMID: 31058226 PMCID: PMC6499549 DOI: 10.1126/sciadv.aav8801] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/19/2019] [Indexed: 05/11/2023]
Abstract
The possibility of imaging single proteins constitutes an exciting challenge for x-ray lasers. Despite encouraging results on large particles, imaging small particles has proven to be difficult for two reasons: not quite high enough pulse intensity from currently available x-ray lasers and, as we demonstrate here, contamination of the aerosolized molecules by nonvolatile contaminants in the solution. The amount of contamination on the sample depends on the initial droplet size during aerosolization. Here, we show that, with our electrospray injector, we can decrease the size of aerosol droplets and demonstrate virtually contaminant-free sample delivery of organelles, small virions, and proteins. The results presented here, together with the increased performance of next-generation x-ray lasers, constitute an important stepping stone toward the ultimate goal of protein structure determination from imaging at room temperature and high temporal resolution.
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Affiliation(s)
- Johan Bielecki
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Max F. Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
- Chemistry Research Laboratory, Department of Chemistry, Oxford University, 12 Mansfield Rd, Oxford OX1 3TA, UK
| | - Benedikt J. Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Hemanth K. N. Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
| | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
| | - Daniel S. D. Larsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
| | - Laura H. Gunn
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Anna Munke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
| | - Jonas A. Sellberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Leonie Flueckiger
- ARC Centre of Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Alberto Pietrini
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
- Division of Scientific Computing, Department of Information Technology, Science for Life Laboratory, Uppsala University, Lägerhyddsvägen 2 (Box 337), SE-751 05 Uppsala, Sweden
| | - Ida Lundholm
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
| | - Gunilla Carlsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
| | - Kenta Okamoto
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
| | - Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120 Uppsala, Sweden
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
| | - Olena Kulyk
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic
| | - Akifumi Higashiura
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, Netherlands
| | - Ne-Te Duane Loh
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
- Department of Physics, National University of Singapore, Singapore, Singapore
| | - Taylor E. Wysong
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Christoph Bostedt
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - Tais Gorkhover
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Bianca Iwan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Institut für Quantenoptik, Leibniz Universität Hannover, Welfengarten 1, 30167 Hannover, Germany
| | - M. Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
| | - Timur Osipov
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Peter Walter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Philip Hart
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Maximilian Bucher
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Anatoli Ulmer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Dipanwita Ray
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Gabriella Carini
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ken R. Ferguson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
| | - Jakob Andreasson
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic
- Condensed Matter Physics, Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic
| | - Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124 Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Corresponding author.
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17
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Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN. Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. Acta Crystallogr F Struct Biol Commun 2019; 75:321-323. [PMID: 31045560 PMCID: PMC6497101 DOI: 10.1107/s2053230x19005909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The policy of IUCr Journals on diffraction data is defined.
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Affiliation(s)
- John R Helliwell
- School of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, United Kingdom
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908-0736, USA
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Randy J Read
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Mark J van Raaij
- CSIC, Centro Nacional de Biotecnologia, c/Darwin 3, Madrid, 28049, Spain
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden
| | - Edward N Baker
- School of Biological Sciences, University of Auckland, School of Biological Sciences, Private Bag 92-019, Auckland, New Zealand
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18
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Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN. Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. J Appl Crystallogr 2019; 52:495-497. [PMID: 31236090 PMCID: PMC6557178 DOI: 10.1107/s1600576719005922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The policy of IUCr Journals on diffraction data is defined.
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Affiliation(s)
- John R Helliwell
- School of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, UK
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908-0736, USA
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Randy J Read
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Mark J van Raaij
- CSIC, Centro Nacional de Biotecnologia, c/Darwin 3, Madrid, 28049, Spain
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden.,The European Extreme Light Infrastructure, Institute of Physics, AS CR, Na Slovance 2, Prague 18221 8, Czech Republic
| | - Edward N Baker
- School of Biological Sciences, University of Auckland, School of Biological Sciences, Private Bag 92-019, Auckland, New Zealand
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19
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Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN. Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography. Acta Crystallogr D Struct Biol 2019; 75:455-457. [PMID: 31063147 PMCID: PMC6503765 DOI: 10.1107/s2059798319004844] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The policy of IUCr Journals on diffraction data is defined.
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Affiliation(s)
- John R Helliwell
- School of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, United Kingdom
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908-0736, USA
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Randy J Read
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Janet Newman
- Collaborative Crystallisation Centre (C3), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Mark J van Raaij
- CSIC, Centro Nacional de Biotecnologia, c/Darwin 3, Madrid, 28049, Spain
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden
| | - Edward N Baker
- School of Biological Sciences, University of Auckland, School of Biological Sciences, Private Bag 92-019, Auckland, New Zealand
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20
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Hantke MF, Bielecki J, Kulyk O, Westphal D, Larsson DSD, Svenda M, Reddy HKN, Kirian RA, Andreasson J, Hajdu J, Maia FRNC. Rayleigh-scattering microscopy for tracking and sizing nanoparticles in focused aerosol beams. IUCrJ 2018; 5:673-680. [PMID: 30443352 PMCID: PMC6211534 DOI: 10.1107/s2052252518010837] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/26/2018] [Indexed: 05/25/2023]
Abstract
Ultra-bright femtosecond X-ray pulses generated by X-ray free-electron lasers (XFELs) can be used to image high-resolution structures without the need for crystallization. For this approach, aerosol injection has been a successful method to deliver 70-2000 nm particles into the XFEL beam efficiently and at low noise. Improving the technique of aerosol sample delivery and extending it to single proteins necessitates quantitative aerosol diagnostics. Here a lab-based technique is introduced for Rayleigh-scattering microscopy allowing us to track and size aerosolized particles down to 40 nm in diameter as they exit the injector. This technique was used to characterize the 'Uppsala injector', which is a pioneering and frequently used aerosol sample injector for XFEL single-particle imaging. The particle-beam focus, particle velocities, particle density and injection yield were measured at different operating conditions. It is also shown how high particle densities and good injection yields can be reached for large particles (100-500 nm). It is found that with decreasing particle size, particle densities and injection yields deteriorate, indicating the need for different injection strategies to extend XFEL imaging to smaller targets, such as single proteins. This work demonstrates the power of Rayleigh-scattering microscopy for studying focused aerosol beams quantitatively. It lays the foundation for lab-based injector development and online injection diagnostics for XFEL research. In the future, the technique may also find application in other fields that employ focused aerosol beams, such as mass spectrometry, particle deposition, fuel injection and three-dimensional printing techniques.
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Affiliation(s)
- Max F. Hantke
- Chemistry Research Laboratory, Department of Chemistry, Oxford University, 12 Mansfield Rd, Oxford OX1 3TA, UK
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Johan Bielecki
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | - Olena Kulyk
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, Prague CZ-18221, Czech Republic
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Daniel S. D. Larsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Hemanth K. N. Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Richard A. Kirian
- Department of Physics, Arizona State University, 550 E. Tyler Drive, Tempe, AZ 85287, USA
| | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, Prague CZ-18221, Czech Republic
- Condensed Matter Physics, Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, Prague CZ-18221, Czech Republic
| | - Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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21
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Wiedorn MO, Oberthür D, Bean R, Schubert R, Werner N, Abbey B, Aepfelbacher M, Adriano L, Allahgholi A, Al-Qudami N, Andreasson J, Aplin S, Awel S, Ayyer K, Bajt S, Barák I, Bari S, Bielecki J, Botha S, Boukhelef D, Brehm W, Brockhauser S, Cheviakov I, Coleman MA, Cruz-Mazo F, Danilevski C, Darmanin C, Doak RB, Domaracky M, Dörner K, Du Y, Fangohr H, Fleckenstein H, Frank M, Fromme P, Gañán-Calvo AM, Gevorkov Y, Giewekemeyer K, Ginn HM, Graafsma H, Graceffa R, Greiffenberg D, Gumprecht L, Göttlicher P, Hajdu J, Hauf S, Heymann M, Holmes S, Horke DA, Hunter MS, Imlau S, Kaukher A, Kim Y, Klyuev A, Knoška J, Kobe B, Kuhn M, Kupitz C, Küpper J, Lahey-Rudolph JM, Laurus T, Le Cong K, Letrun R, Xavier PL, Maia L, Maia FRNC, Mariani V, Messerschmidt M, Metz M, Mezza D, Michelat T, Mills G, Monteiro DCF, Morgan A, Mühlig K, Munke A, Münnich A, Nette J, Nugent KA, Nuguid T, Orville AM, Pandey S, Pena G, Villanueva-Perez P, Poehlsen J, Previtali G, Redecke L, Riekehr WM, Rohde H, Round A, Safenreiter T, Sarrou I, Sato T, Schmidt M, Schmitt B, Schönherr R, Schulz J, Sellberg JA, Seibert MM, Seuring C, Shelby ML, Shoeman RL, Sikorski M, Silenzi A, Stan CA, Shi X, Stern S, Sztuk-Dambietz J, Szuba J, Tolstikova A, Trebbin M, Trunk U, Vagovic P, Ve T, Weinhausen B, White TA, Wrona K, Xu C, Yefanov O, Zatsepin N, Zhang J, Perbandt M, Mancuso AP, Betzel C, Chapman H, Barty A. Megahertz serial crystallography. Nat Commun 2018; 9:4025. [PMID: 30279492 PMCID: PMC6168542 DOI: 10.1038/s41467-018-06156-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 08/21/2018] [Indexed: 01/08/2023] Open
Abstract
The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.
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Grants
- Project oriented funds Helmholtz-Gemeinschaft (Helmholtz Gemeinschaft)
- DFG-EXC1074 Deutsche Forschungsgemeinschaft (German Research Foundation)
- R01 GM117342 NIGMS NIH HHS
- R01 GM095583 NIGMS NIH HHS
- 609920 European Research Council
- Wellcome Trust
- : The Helmholtz organisation through program oriented funds; excellence cluster "The Hamburg Center for Ultrafast Imaging – Structure, Dynamics and Control of Matter at the Atomic Scale" of the Deutsche Forschungsgemeinschaft (CUI, DFG-EXC1074); the European Research Council, “Frontiers in Attosecond X-ray Science: Imaging and Spectroscopy (AXSIS)”, ERC-2013-SyG 609920 (2014-2018); the Gottfried Wilhelm Leibniz Program of the DFG; the project “X-probe” funded by the European Union’s 2020 Research and Innovation Program under the Marie Sklodowska-Curie grant agreement 637295; the BMBF German-Russian Cooperation “SyncFELMed” grant 05K14CHA; European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the Consolidator Grant COMOTION (ERC-614507-Küpper); the Helmholtz Gemeinschaft through the "Impuls und Vernetzungsfond"; Helmholtz Initiative and Networking Fund through the Young Investigators Program and by the Deutsche Forschungsgemeinschaft SFB755/B03; the Swedish Research Council; the Knut and Alice Wallenberg Foundation; the Röntgen-Angström Cluster; the BMBF via projects 05K13GU7 and 05E13GU1; the from Ministry of Education, Science, Research and Sport of the Slovak Republic; the Joachim Herz Stiftung; the Deutsche Forschungsgemeinschaft (DFG) Cluster of Excellence “Inflammation at interfaces” (EXC 306); the Swedish Research Council; the Swedish Foundation for Strategic Research; the Australian Research Council Centre of Excellence in Advanced Molecular Imaging [CE140100011]; the Australian Nuclear Science and Technology Organisation (ANSTO); the International Synchrotron Access Program (ISAP) managed by the Australian Synchrotron, part of ANSTO, and funded by the Australian Government; The projects Structural dynamics of biomolecular systems (CZ.02.1.01/0.0/0.0/15_003/0000447) (ELIBIO) and Advanced research using high intensity laser produced photons and particles (CZ.02.1.01/0.0/0.0/16_019/0000789) (ADONIS) from European Regional Development Fund, the Ministry of Education, Youth and Sports as part of targeted support from the National Programme of Sustainability II; the Röntgen Ångström Cluster; the Chalmers Area of Advance, Material science; the Project DPI2016-78887-C3-1-R, Ministerio de Economía y Competitividad; the Wellcome Trust (studentship 075491/04); Rutgers University, Newark; the Max Planck Society; the NSF-STC “BioXFEL” through award STC-1231306; the Slovak Research and Development Agency under contract APVV-14-0181; the Wellcome Trust; Helmholtz Strategic Investment funds; Australian Research Council Centre of Excellence in Advanced Molecular Imaging [CE140100011], Australian Nuclear Science and Technology Organisation (ANSTO); The Swedish Research Council, the Knut and Alice Wallenberg Foundation, and the Röntgen-Angström Cluster, BMBF via projects 05K13GU7 and 05E13GU1, Ministry of Education, Science, Research and Sport of the Slovak Republic; BMBF grants 05K16GUA and 05K12GU3; the Joachim Herz Foundation through and Add-on Fellowship; NHMRC project grants 1107804 and 1108859, ARC Discovery Early Career Research Award (DE170100783); National Health and Medical Research Council (NHMRC grants 1107804, 1071659). BK is NHMRC Principal Research Fellow (1110971); National Science Foundation Grant # 1565180, "ABI Innovation: New Algorithms for Biological X-ray Free Electron Laser Data"; Diamond Light Source and from a Strategic Award from the Wellcome Trust and the Biotechnology and Biological Sciences Research Council (grant 102593); use of the XBI biological sample preparation laboratory, enabled by the XBI User Consortium. This work was performed, in part, under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. MLS, MAC and MF were supported by NIH grant 1R01GM117342-01
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Affiliation(s)
- Max O Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Robin Schubert
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
- Integrated Biology Infrastructure Life-Science Facility at the European XFEL (XBI), Holzkoppel 4, 22869, Schenefeld, Germany
| | - Nadine Werner
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | - Brian Abbey
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Luigi Adriano
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Aschkan Allahgholi
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- ELI Beamlines, Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21, Prague, Czech Republic
- Condensed Matter Physics, Department of Physics, Chalmers University of Technology, Gothenburg, 412 96, Sweden
| | - Steve Aplin
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Kartik Ayyer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Saša Bajt
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Imrich Barák
- Institute of Molecular Biology, SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Sabine Botha
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sandor Brockhauser
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Igor Cheviakov
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Francisco Cruz-Mazo
- Depart. Ingeniería Aeroespacial y Mecánica de Fluidos ETSI, Universidad de Sevilla, 41092, Sevilla, Spain
| | | | - Connie Darmanin
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - R Bruce Doak
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Katerina Dörner
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Yang Du
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Hans Fangohr
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Engineering and the Environment, University of Southampton, SO17 1BJ, Southampton, UK
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - Alfonso M Gañán-Calvo
- Depart. Ingeniería Aeroespacial y Mecánica de Fluidos ETSI, Universidad de Sevilla, 41092, Sevilla, Spain
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Hamburg University of Technology, Vision Systems E-2, Harburger Schloßstr. 20, 21079, Hamburg, Germany
| | | | - Helen Mary Ginn
- Division of Structural Biology, Headington, Oxford, OX3 7BN, UK
- Diamond Light Source, Research Complex at Harwell, and University of Oxford, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Heinz Graafsma
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Mid Sweden University, Holmgatan 10, 85170, Sundsvall, Sweden
| | - Rita Graceffa
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Lars Gumprecht
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Peter Göttlicher
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- ELI Beamlines, Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21, Prague, Czech Republic
| | - Steffen Hauf
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Michael Heymann
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Susannah Holmes
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Daniel A Horke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA
| | - Siegfried Imlau
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alexander Klyuev
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Juraj Knoška
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Manuela Kuhn
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Christopher Kupitz
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Jochen Küpper
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, Universität Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany
| | - Janine Mia Lahey-Rudolph
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Torsten Laurus
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Karoline Le Cong
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Luis Maia
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, 94720, CA, USA
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Markus Metz
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Davide Mezza
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Thomas Michelat
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Grant Mills
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Diana C F Monteiro
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Andrew Morgan
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Kerstin Mühlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Anna Munke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Astrid Münnich
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Julia Nette
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Keith A Nugent
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Theresa Nuguid
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | - Allen M Orville
- Diamond Light Source, Research Complex at Harwell, and University of Oxford, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Gisel Pena
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Pablo Villanueva-Perez
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jennifer Poehlsen
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Lars Redecke
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Winnie Maria Riekehr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tatiana Safenreiter
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Tokushi Sato
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Bernd Schmitt
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Robert Schönherr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Jonas A Sellberg
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm, 106 91, Sweden
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
| | - Carolin Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Megan L Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Robert L Shoeman
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Claudiu A Stan
- Physics Department, Rutgers University Newark, Newark, NJ, 07102, USA
| | - Xintian Shi
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Stephan Stern
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Janusz Szuba
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Martin Trebbin
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, University at Buffalo, 359 Natural Sciences Complex, Buffalo, NY, 14260, USA
- Institute of Nanostructure and Solid State Physics, Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Ulrich Trunk
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Patrik Vagovic
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD, 4222, Australia
| | | | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Krzysztof Wrona
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Chen Xu
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ, 85287, USA
| | - Jiaguo Zhang
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Markus Perbandt
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | | | - Christian Betzel
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
- Integrated Biology Infrastructure Life-Science Facility at the European XFEL (XBI), Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
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22
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Lundholm IV, Sellberg JA, Ekeberg T, Hantke MF, Okamoto K, van der Schot G, Andreasson J, Barty A, Bielecki J, Bruza P, Bucher M, Carron S, Daurer BJ, Ferguson K, Hasse D, Krzywinski J, Larsson DSD, Morgan A, Mühlig K, Müller M, Nettelblad C, Pietrini A, Reddy HKN, Rupp D, Sauppe M, Seibert M, Svenda M, Swiggers M, Timneanu N, Ulmer A, Westphal D, Williams G, Zani A, Faigel G, Chapman HN, Möller T, Bostedt C, Hajdu J, Gorkhover T, Maia FRNC. Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging. IUCrJ 2018; 5:531-541. [PMID: 30224956 PMCID: PMC6126651 DOI: 10.1107/s2052252518010047] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/11/2018] [Indexed: 05/19/2023]
Abstract
Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. The anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.
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Affiliation(s)
- Ida V. Lundholm
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Jonas A. Sellberg
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | | | - Kenta Okamoto
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, CZ-182 21 Prague, Czech Republic
- Condensed Matter Physics, Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Johan Bielecki
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Petr Bruza
- Condensed Matter Physics, Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Max Bucher
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Sebastian Carron
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
| | - Benedikt J. Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Ken Ferguson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
- PULSE Institute and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Jacek Krzywinski
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
| | - Daniel S. D. Larsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Andrew Morgan
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kerstin Mühlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Maria Müller
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Division of Scientific Computing, Department of Information Technology, Science for Life Laboratory, Uppsala University, Lagerhyddsvägen 2 (Box 337), SE-751 05 Uppsala, Sweden
| | - Alberto Pietrini
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Hemanth K. N. Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Daniela Rupp
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - Mario Sauppe
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Michelle Swiggers
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
| | - Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Anatoli Ulmer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Garth Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
- NSLS-II, Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973, USA
| | - Alessandro Zani
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Gyula Faigel
- Research Institute for Solid State Physics and Optics, 1525 Budapest, Hungary
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas Möller
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - Christoph Bostedt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
- PULSE Institute and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Physics, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, CZ-182 21 Prague, Czech Republic
| | - Tais Gorkhover
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
- PULSE Institute and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
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23
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Allen AJ, Hajdu J, McIntyre GJ. Journal of Applied Crystallography: the first 50 years and beyond. J Appl Crystallogr 2018. [DOI: 10.1107/s1600576718004478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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24
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Okamoto K, Miyazaki N, Song C, Maia FRNC, Reddy HKN, Abergel C, Claverie JM, Hajdu J, Svenda M, Murata K. Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy. Sci Rep 2017; 7:13291. [PMID: 29038566 PMCID: PMC5643343 DOI: 10.1038/s41598-017-13390-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/22/2017] [Indexed: 12/23/2022] Open
Abstract
The Pithoviridae giant virus family exhibits the largest viral particle known so far, a prolate spheroid up to 2.5 μm in length and 0.9 μm in diameter. These particles show significant variations in size. Little is known about the structure of the intact virion due to technical limitations with conventional electron cryo-microscopy (cryo-EM) when imaging thick specimens. Here we present the intact structure of the giant Pithovirus sibericum particle at near native conditions using high-voltage electron cryo-tomography (cryo-ET) and energy-filtered cryo-EM. We detected a previously undescribed low-density outer layer covering the tegument and a periodical structuring of the fibres in the striated apical cork. Energy-filtered Zernike phase-contrast cryo-EM images show distinct substructures inside the particles, implicating an internal compartmentalisation. The density of the interior volume of Pithovirus particles is three quarters lower than that of the Mimivirus. However, it is remarkably high given that the 600 kbp Pithovirus genome is only half the size of the Mimivirus genome and is packaged in a volume up to 100 times larger. These observations suggest that the interior is densely packed with macromolecules in addition to the genomic nucleic acid.
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Affiliation(s)
- Kenta Okamoto
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.
| | - Naoyuki Miyazaki
- National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585, Japan
| | - Chihong Song
- National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585, Japan
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Hemanth K N Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Chantal Abergel
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, 13288, France
| | - Jean-Michel Claverie
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, 13288, France.,Assistance Publique des Hôpitaux de Marseille. La Timone, 13005, Marseille, France
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.,Institute of Physics AS CR, v.v.i., Na Slovance 2, 18221, Prague 8, Czech Republic
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585, Japan.
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25
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26
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Daurer BJ, Okamoto K, Bielecki J, Maia FRNC, Mühlig K, Seibert MM, Hantke MF, Nettelblad C, Benner WH, Svenda M, Tîmneanu N, Ekeberg T, Loh ND, Pietrini A, Zani A, Rath AD, Westphal D, Kirian RA, Awel S, Wiedorn MO, van der Schot G, Carlsson GH, Hasse D, Sellberg JA, Barty A, Andreasson J, Boutet S, Williams G, Koglin J, Andersson I, Hajdu J, Larsson DSD. Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses. IUCrJ 2017; 4:251-262. [PMID: 28512572 PMCID: PMC5414399 DOI: 10.1107/s2052252517003591] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/07/2017] [Indexed: 05/25/2023]
Abstract
This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. Aerosolized Omono River virus particles of ∼40 nm in diameter were injected into the submicrometre X-ray focus at a reduced pressure. Diffraction patterns were recorded on two area detectors. The statistical nature of the measurements from many individual particles provided information about the intensity profile of the X-ray beam, phase variations in the wavefront and the size distribution of the injected particles. The results point to a wider than expected size distribution (from ∼35 to ∼300 nm in diameter). This is likely to be owing to nonvolatile contaminants from larger droplets during aerosolization and droplet evaporation. The results suggest that the concentration of nonvolatile contaminants and the ratio between the volumes of the initial droplet and the sample particles is critical in such studies. The maximum beam intensity in the focus was found to be 1.9 × 1012 photons per µm2 per pulse. The full-width of the focus at half-maximum was estimated to be 500 nm (assuming 20% beamline transmission), and this width is larger than expected. Under these conditions, the diffraction signal from a sample-sized particle remained above the average background to a resolution of 4.25 nm. The results suggest that reducing the size of the initial droplets during aerosolization is necessary to bring small particles into the scope of detailed structural studies with X-ray lasers.
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Affiliation(s)
- Benedikt J. Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Kenta Okamoto
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Johan Bielecki
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kerstin Mühlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - M. Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Max F. Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Carl Nettelblad
- Division of Scientific Computing, Department of Information Technology, Science for Life Laboratory, Uppsala University, Lägerhyddsvägen 2 (Box 337), SE-751 05 Uppsala, Sweden
| | - W. Henry Benner
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Nicuşor Tîmneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Molecular and Condensed Matter Physics, Department of Physics and Astronomy, Uppsala University, Lägerhyddsvägen 1 (Box 516), SE-751 20 Uppsala, Sweden
| | - Tomas Ekeberg
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - N. Duane Loh
- Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Alberto Pietrini
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Alessandro Zani
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Asawari D. Rath
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Bhabha Atomic Research Center, Mumbai 400 085, India
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Richard A. Kirian
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Salah Awel
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Gunilla H. Carlsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Jonas A. Sellberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Garth Williams
- Brookhaven National Laboratory, 743 Brookhaven Avenue, Upton, NY 11973, USA
| | - Jason Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21 Prague 8, Czech Republic
| | - Daniel S. D. Larsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
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27
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van der Schot G, Svenda M, Maia FRNC, Hantke MF, DePonte DP, Seibert MM, Aquila A, Schulz J, Kirian RA, Liang M, Stellato F, Bari S, Iwan B, Andreasson J, Timneanu N, Bielecki J, Westphal D, Nunes de Almeida F, Odić D, Hasse D, Carlsson GH, Larsson DSD, Barty A, Martin AV, Schorb S, Bostedt C, Bozek JD, Carron S, Ferguson K, Rolles D, Rudenko A, Epp SW, Foucar L, Rudek B, Erk B, Hartmann R, Kimmel N, Holl P, Englert L, Loh ND, Chapman HN, Andersson I, Hajdu J, Ekeberg T. Open data set of live cyanobacterial cells imaged using an X-ray laser. Sci Data 2016; 3:160058. [PMID: 27479514 PMCID: PMC4968219 DOI: 10.1038/sdata.2016.58] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/18/2016] [Indexed: 01/20/2023] Open
Abstract
Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.
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Affiliation(s)
- Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Max F Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Daniel P DePonte
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Andrew Aquila
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Joachim Schulz
- European XFEL, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Richard A Kirian
- Arizona State University, Physics Department, PO Box 871504, Tempe, Arizona 85287-1504, USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Francesco Stellato
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,I.N.F.N. and Physics Department, University of Rome 'Tor Vergata', Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Sadia Bari
- European XFEL, Albert-Einstein-Ring 19, 22761 Hamburg, Germany.,Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Bianca Iwan
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.,ELI beamlines, Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 18221 Prague, Czech Republic
| | - Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.,Department of Physics and Astronomy, Uppsala University, Lägerhyddsvägen 1, Box 516, SE-751 20 Uppsala, Sweden
| | - Johan Bielecki
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | | | - Duško Odić
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.,Center for Technology Transfer and Innovation, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Gunilla H Carlsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Daniel S D Larsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrew V Martin
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, The University of Melbourne, Victoria 3010, Australia
| | - Sebastian Schorb
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - John D Bozek
- Synchrotron SOLEIL, L'orme des Merisiers roundabout of St Aubin, 91190 Saint Aubin, France
| | - Sebastian Carron
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Ken Ferguson
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Daniel Rolles
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Artem Rudenko
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Sascha W Epp
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Lutz Foucar
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Benedikt Rudek
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Benjamin Erk
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | | | - Nils Kimmel
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany.,Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | - Peter Holl
- PNSensor GmbH, Otto-Hahn-Ring 6, 81739 Munich, Germany
| | - Lars Englert
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany.,Ultrafast Coherent Dynamics Group, University Oldenburg, Carl-von-Ossietzky Strasse 9-11, 26129 Oldenburg, Germany
| | - N Duane Loh
- Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4 Blk S1 A, Singapore 117546, Singapore
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,University of Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.,European XFEL, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
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Abstract
The latest virtual special issue ofJournal of Applied Crystallography(http://journals.iucr.org/special_issues/2016/ccpfel) collects software for free-electron laser research and presents tools for a range of topics such as simulation of experiments, online monitoring of data collection, selection of hits, diagnostics of data quality, data management, data analysis and structure determination for both nanocrystallography and single-particle diffractive imaging. This article provides an introduction to the special issue.
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Hantke MF, Hasse D, Ekeberg T, John K, Svenda M, Loh D, Martin AV, Timneanu N, Larsson DSD, van der Schot G, Carlsson GH, Ingelman M, Andreasson J, Westphal D, Iwan B, Uetrecht C, Bielecki J, Liang M, Stellato F, DePonte DP, Bari S, Hartmann R, Kimmel N, Kirian RA, Seibert MM, Mühlig K, Schorb S, Ferguson K, Bostedt C, Carron S, Bozek JD, Rolles D, Rudenko A, Foucar L, Epp SW, Chapman HN, Barty A, Andersson I, Hajdu J, Maia FRNC. A data set from flash X-ray imaging of carboxysomes. Sci Data 2016; 3:160061. [PMID: 27479842 DOI: 10.1038/nphoton.2014.270] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/01/2016] [Indexed: 05/26/2023] Open
Abstract
Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.
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Affiliation(s)
- Max F Hantke
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Dirk Hasse
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Tomas Ekeberg
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Katja John
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Martin Svenda
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Duane Loh
- Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Andrew V Martin
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, The University of Melbourne, Victoria 3010, Australia
| | - Nicusor Timneanu
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- Department of Physics and Astronomy, Uppsala University, Lägerhyddsvägen 1, Box 516, Uppsala SE- 751 20, Sweden
| | - Daniel S D Larsson
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Gijs van der Schot
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Gunilla H Carlsson
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Margareta Ingelman
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Jakob Andreasson
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- ELI beamlines, Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, Prague 18221, Czech Republic
| | - Daniel Westphal
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Bianca Iwan
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Charlotte Uetrecht
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Johan Bielecki
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Mengning Liang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Francesco Stellato
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- I.N.F.N. and Physics Department, University of Rome 'Tor Vergata', Via della Ricerca Scientifica 1, Rome 00133, Italy
| | - Daniel P DePonte
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Sadia Bari
- European XFEL GmbH, Albert-Einstein-Ring 19, Hamburg 22761, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, Hamburg 22607, Germany
| | | | - Nils Kimmel
- Max Planck Institute for Extraterrestrial Physics, Giessenbachstrasse, Garching 85741, Germany
| | - Richard A Kirian
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - M Marvin Seibert
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Kerstin Mühlig
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Sebastian Schorb
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Ken Ferguson
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Sebastian Carron
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - John D Bozek
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Daniel Rolles
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- Department of Physics, J.R. Macdonald Laboratory, Kansas State University, Cardwell Hall, Manhattan, Kansas 66506, USA
- Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, Hamburg 22607, Germany
| | - Artem Rudenko
- Department of Physics, J.R. Macdonald Laboratory, Kansas State University, Cardwell Hall, Manhattan, Kansas 66506, USA
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, Hamburg 22607, Germany
- Max Planck Institute for Nuclear Physics, Saupfercheckweg 1, Heidelberg 69117, Germany
| | - Lutz Foucar
- Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, Hamburg 22607, Germany
| | - Sascha W Epp
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, Hamburg 22607, Germany
- Max Planck Institute for Nuclear Physics, Saupfercheckweg 1, Heidelberg 69117, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Inger Andersson
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Janos Hajdu
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- European XFEL GmbH, Albert-Einstein-Ring 19, Hamburg 22761, Germany
| | - Filipe R N C Maia
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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30
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Munke A, Andreasson J, Aquila A, Awel S, Ayyer K, Barty A, Bean RJ, Berntsen P, Bielecki J, Boutet S, Bucher M, Chapman HN, Daurer BJ, DeMirci H, Elser V, Fromme P, Hajdu J, Hantke MF, Higashiura A, Hogue BG, Hosseinizadeh A, Kim Y, Kirian RA, Reddy HKN, Lan TY, Larsson DSD, Liu H, Loh ND, Maia FRNC, Mancuso AP, Mühlig K, Nakagawa A, Nam D, Nelson G, Nettelblad C, Okamoto K, Ourmazd A, Rose M, van der Schot G, Schwander P, Seibert MM, Sellberg JA, Sierra RG, Song C, Svenda M, Timneanu N, Vartanyants IA, Westphal D, Wiedorn MO, Williams GJ, Xavier PL, Yoon CH, Zook J. Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source. Sci Data 2016; 3:160064. [PMID: 27478984 PMCID: PMC4968191 DOI: 10.1038/sdata.2016.64] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/22/2016] [Indexed: 11/09/2022] Open
Abstract
Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.
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Affiliation(s)
- Anna Munke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden.,Institute of Physics ASCR, v.v.i. (FZU), ELI-Beamlines Project, Prague 182 21, Czech Republic
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Salah Awel
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
| | - Kartik Ayyer
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
| | - Anton Barty
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
| | - Richard J Bean
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | - Peter Berntsen
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Johan Bielecki
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Maximilian Bucher
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.,Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA.,Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstraße 36, Berlin 10623, Germany
| | - Henry N Chapman
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany.,Department of Physics, University of Hamburg, Hamburg 22761, Germany
| | - Benedikt J Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Hasan DeMirci
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.,Stanford PULSE Institute, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Veit Elser
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA
| | - Petra Fromme
- Arizona State University, School of Molecular Sciences (SMS), Tempe, Arizona 85287-1604, USA.,Biodesign Center for Applied Structural Discovery, Biodesign Institute at Arizona State University, Tempe 85287, USA
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Max F Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Akifumi Higashiura
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Brenda G Hogue
- Biodesign Center for Applied Structural Discovery, Biodesign Institute at Arizona State University, Tempe 85287, USA.,Arizona State University, School of Life Sciences (SOLS), Tempe, Arizona 85287-5401, USA.,Biodesign Center for Infectious Diseases and Vaccinology, Biodesign Institute at Arizona State University, Tempe 85287, USA
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, USA
| | - Yoonhee Kim
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Richard A Kirian
- Biodesign Center for Applied Structural Discovery, Biodesign Institute at Arizona State University, Tempe 85287, USA.,Arizona State University, Department of Physics, Tempe, Arizona 85287, USA
| | - Hemanth K N Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Ti-Yen Lan
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA
| | - Daniel S D Larsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Haiguang Liu
- Beijing Computational Science Research Center, 8 W Dongbeiwang Rd, Haidian, Beijing 100193, China
| | - N Duane Loh
- Centre for Bio-imaging Sciences, National University of Singapore, 14 Science Drive 4, BLK S1A, Singapore 117543, Singapore
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | | | - Kerstin Mühlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Daewoong Nam
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Garrett Nelson
- Arizona State University, Department of Physics, Tempe, Arizona 85287, USA
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden.,Department of Information Technology, Science for Life Laboratory, Uppsala University, Lägerhyddsvägen 2 (Box 337), Uppsala SE-75105, Sweden
| | - Kenta Okamoto
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, USA
| | - Max Rose
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg D-22607, Germany
| | - Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Peter Schwander
- Department of Physics, University of Wisconsin Milwaukee, 3135 North Maryland Ave., Milwaukee, Wisconsin 53211, USA
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Jonas A Sellberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden.,Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm SE-106 91, Sweden
| | - Raymond G Sierra
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.,Stanford PULSE Institute, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Changyong Song
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden.,Department of Physics and Astronomy, Uppsala University, Lägerhyddsvägen 1 (Box 516), Uppsala SE-75120, Sweden
| | - Ivan A Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg D-22607, Germany.,National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe shosse 31, Moscow 115409, Russia
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-75124, Sweden
| | - Max O Wiedorn
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany.,Department of Physics, University of Hamburg, Hamburg 22761, Germany
| | - Garth J Williams
- Brookhaven National Laboratory, NSLS-II, Upton, New York 11973, USA
| | - Paulraj Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany.,Department of Physics, University of Hamburg, Hamburg 22761, Germany.,Max-Planck Institute for the Structure and Dynamics of Matter, CFEL, Hamburg 22607, Germany
| | - Chun Hong Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - James Zook
- Arizona State University, School of Molecular Sciences (SMS), Tempe, Arizona 85287-1604, USA.,Biodesign Center for Applied Structural Discovery, Biodesign Institute at Arizona State University, Tempe 85287, USA
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31
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Abstract
Today Scientific Data launched a collection of publications describing data from X-ray free-electron lasers under the theme ‘Structural Biology Applications of X-ray Lasers’. The papers cover data on nanocrystals, single virus particles, isolated cell organelles, and living cells. All data are deposited with the Coherent X-ray Imaging Data Bank (CXIDB) and available to the scientific community to develop ideas, tools and procedures to meet challenges with the expected torrents of data from new X-ray lasers, capable of producing billion exposures per day.
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Affiliation(s)
- Filipe R N C Maia
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Janos Hajdu
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
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32
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Szőke A, Hajdu J. Energy utilization in fluctuating biological energy converters. Struct Dyn 2016; 3:034701. [PMID: 27191009 PMCID: PMC4851624 DOI: 10.1063/1.4945792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 05/03/2016] [Accepted: 03/30/2016] [Indexed: 06/05/2023]
Abstract
We have argued previously [Szoke et al., FEBS Lett. 553, 18-20 (2003); Curr. Chem. Biol. 1, 53-57 (2007)] that energy utilization and evolution are emergent properties based on a small number of established laws of physics and chemistry. The relevant laws constitute a framework for biology on a level intermediate between quantum chemistry and cell biology. There are legitimate questions whether these concepts are valid at the mesoscopic level. Such systems fluctuate appreciably, so it is not clear what their efficiency is. Advances in fluctuation theorems allow the description of such systems on a molecular level. We attempt to clarify this topic and bridge the biochemical and physical descriptions of mesoscopic systems.
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Affiliation(s)
- Abraham Szőke
- Lawrence Livermore National Laboratory , Livermore, California 94551, USA
| | - Janos Hajdu
- Department of Cell and Molecular Biology, Uppsala University , Box 596, S-75124 Uppsala, Sweden
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33
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Aquila A, Barty A, Bostedt C, Boutet S, Carini G, dePonte D, Drell P, Doniach S, Downing KH, Earnest T, Elmlund H, Elser V, Gühr M, Hajdu J, Hastings J, Hau-Riege SP, Huang Z, Lattman EE, Maia FRNC, Marchesini S, Ourmazd A, Pellegrini C, Santra R, Schlichting I, Schroer C, Spence JCH, Vartanyants IA, Wakatsuki S, Weis WI, Williams GJ. The linac coherent light source single particle imaging road map. Struct Dyn 2015; 2:041701. [PMID: 26798801 PMCID: PMC4711616 DOI: 10.1063/1.4918726] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 04/06/2015] [Indexed: 05/19/2023]
Abstract
Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLS held a workshop to discuss the scientific and technical challenges for reaching the ultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap toward reaching atomic resolution, 3D imaging at free-electron laser sources.
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Affiliation(s)
| | - A Barty
- Center for Free-Electron Laser Science, DESY , Notkestr. 85, 22607 Hamburg, Germany
| | - C Bostedt
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - S Boutet
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - G Carini
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - D dePonte
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | | | - K H Downing
- Lawrence Berkeley National Laboratory , 1 Cyclotron Rd., Berkeley, California 94720, USA
| | | | | | | | - M Gühr
- PULSE Institute , SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | - J Hastings
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - S P Hau-Riege
- Lawrence Livermore National Laboratory , Livermore, California 94550, USA
| | - Z Huang
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | | | - S Marchesini
- Lawrence Berkeley National Laboratory , 1 Cyclotron Rd., Berkeley, California 94720, USA
| | - A Ourmazd
- Department of Physics, University of Wisconsin Milwaukee , 1900 E. Kenwood Blvd, Milwaukee, Wisconsin 53211, USA
| | | | | | - I Schlichting
- Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - C Schroer
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85, 22607 Hamburg, Germany
| | - J C H Spence
- Department of Physics, Arizona State University , Rural Rd, Tempe, Arizona 85287, USA
| | | | | | - W I Weis
- School of Medicine, Stanford University , 299 Campus Drive, Stanford, California 94305, USA
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34
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Ekeberg T, Svenda M, Abergel C, Maia FRNC, Seltzer V, Claverie JM, Hantke M, Jönsson O, Nettelblad C, van der Schot G, Liang M, DePonte DP, Barty A, Seibert MM, Iwan B, Andersson I, Loh ND, Martin AV, Chapman H, Bostedt C, Bozek JD, Ferguson KR, Krzywinski J, Epp SW, Rolles D, Rudenko A, Hartmann R, Kimmel N, Hajdu J. Three-dimensional reconstruction of the giant mimivirus particle with an x-ray free-electron laser. Phys Rev Lett 2015; 114:098102. [PMID: 25793853 DOI: 10.1103/physrevlett.114.098102] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Indexed: 05/19/2023]
Abstract
We present a proof-of-concept three-dimensional reconstruction of the giant mimivirus particle from experimentally measured diffraction patterns from an x-ray free-electron laser. Three-dimensional imaging requires the assembly of many two-dimensional patterns into an internally consistent Fourier volume. Since each particle is randomly oriented when exposed to the x-ray pulse, relative orientations have to be retrieved from the diffraction data alone. We achieve this with a modified version of the expand, maximize and compress algorithm and validate our result using new methods.
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Affiliation(s)
- Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Chantal Abergel
- Génomique & Structurale - IGS - UMR 7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Parc Scientifique de Luminy, Case 934, 13288 Marseille Cedex 9, France
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Virginie Seltzer
- Génomique & Structurale - IGS - UMR 7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Parc Scientifique de Luminy, Case 934, 13288 Marseille Cedex 9, France
| | - Jean-Michel Claverie
- Génomique & Structurale - IGS - UMR 7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Parc Scientifique de Luminy, Case 934, 13288 Marseille Cedex 9, France
| | - Max Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Olof Jönsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Mengning Liang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel P DePonte
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Bianca Iwan
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Attophysics Group, CEA-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - N Duane Loh
- Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4 Blk S1 A, Singapore 117546, Singapore
| | - Andrew V Martin
- The University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Henry Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- University of Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - John D Bozek
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Ken R Ferguson
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Jacek Krzywinski
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Sascha W Epp
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel Rolles
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- J. R. Macdonald Laboratory, Department of Physics, Kansas State University, 116 Cardwell Hall, Manhattan, Kansas 66506, USA
| | - Artem Rudenko
- J. R. Macdonald Laboratory, Department of Physics, Kansas State University, 116 Cardwell Hall, Manhattan, Kansas 66506, USA
| | | | - Nils Kimmel
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- European XFEL, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
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35
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van der Schot G, Svenda M, Maia FRNC, Hantke M, DePonte DP, Seibert MM, Aquila A, Schulz J, Kirian R, Liang M, Stellato F, Iwan B, Andreasson J, Timneanu N, Westphal D, Almeida FN, Odic D, Hasse D, Carlsson GH, Larsson DSD, Barty A, Martin AV, Schorb S, Bostedt C, Bozek JD, Rolles D, Rudenko A, Epp S, Foucar L, Rudek B, Hartmann R, Kimmel N, Holl P, Englert L, Duane Loh NT, Chapman HN, Andersson I, Hajdu J, Ekeberg T. Imaging single cells in a beam of live cyanobacteria with an X-ray laser. Nat Commun 2015; 6:5704. [PMID: 25669616 DOI: 10.1038/ncomms6704] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 10/29/2014] [Indexed: 01/01/2023] Open
Abstract
There exists a conspicuous gap of knowledge about the organization of life at mesoscopic levels. Ultra-fast coherent diffractive imaging with X-ray free-electron lasers can probe structures at the relevant length scales and may reach sub-nanometer resolution on micron-sized living cells. Here we show that we can introduce a beam of aerosolised cyanobacteria into the focus of the Linac Coherent Light Source and record diffraction patterns from individual living cells at very low noise levels and at high hit ratios. We obtain two-dimensional projection images directly from the diffraction patterns, and present the results as synthetic X-ray Nomarski images calculated from the complex-valued reconstructions. We further demonstrate that it is possible to record diffraction data to nanometer resolution on live cells with X-ray lasers. Extension to sub-nanometer resolution is within reach, although improvements in pulse parameters and X-ray area detectors will be necessary to unlock this potential.
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Affiliation(s)
- Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Filipe R N C Maia
- 1] Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden [2] Lawrence Berkeley National Lab, 1 Cyclotron Road Mail Stop 943-256, Berkeley, California 94720, USA
| | - Max Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Daniel P DePonte
- 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - M Marvin Seibert
- 1] Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden [2] LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Andrew Aquila
- 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] The European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Joachim Schulz
- 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] The European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Richard Kirian
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Mengning Liang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Francesco Stellato
- 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] I.N.F.N. and Physics Department, University of Rome 'Tor Vergata', Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Bianca Iwan
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - F Nunes Almeida
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Dusko Odic
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Gunilla H Carlsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Daniel S D Larsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Anton Barty
- Lawrence Berkeley National Lab, 1 Cyclotron Road Mail Stop 943-256, Berkeley, California 94720, USA
| | - Andrew V Martin
- 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] ARC Centre of Excellence for Coherent X-ray Science, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sebastian Schorb
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - John D Bozek
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Daniel Rolles
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Artem Rudenko
- 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] Department of Physics, Kansas State University, 331 Cardwell Hall, Manhattan, Kansas 66506, USA
| | - Sascha Epp
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lutz Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Benedikt Rudek
- Physikalisch-Technische Bundesanstalt (PTB) Bundesallee 100, 38116 Braunschweig, Germany
| | | | - Nils Kimmel
- 1] PNSensor GmbH, Römerstrasse 28, 80803 München, Germany [2] Max Planck Institute for Extraterrestrial Physics, Giessenbachstrasse, 85741 Garching, Germany
| | - Peter Holl
- PNSensor GmbH, Römerstrasse 28, 80803 München, Germany
| | - Lars Englert
- Institute of Physics, Carl von Ossietzky Universitaet Oldenburg, Carl-von-Ossietzky-Straße 9-11, D-26129 Oldenburg, Germany
| | - Ne-Te Duane Loh
- Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Henry N Chapman
- 1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany [2] University of Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Janos Hajdu
- 1] Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden [2] The European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
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Rath AD, Timneanu N, Maia FRNC, Bielecki J, Fleckenstein H, Iwan B, Svenda M, Hasse D, Carlsson G, Westphal D, Mühlig K, Hantke M, Ekeberg T, Seibert MM, Zani A, Liang M, Stellato F, Kirian R, Bean R, Barty A, Galli L, Nass K, Barthelmess M, Aquila A, Toleikis S, Treusch R, Roling S, Wöstmann M, Zacharias H, Chapman HN, Bajt S, DePonte D, Hajdu J, Andreasson J. Explosion dynamics of sucrose nanospheres monitored by time of flight spectrometry and coherent diffractive imaging at the split-and-delay beam line of the FLASH soft X-ray laser. Opt Express 2014; 22:28914-28925. [PMID: 25402130 DOI: 10.1364/oe.22.028914] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We use a Mach-Zehnder type autocorrelator to split and delay XUV pulses from the FLASH soft X-ray laser for triggering and subsequently probing the explosion of aerosolised sugar balls. FLASH was running at 182 eV photon energy with pulses of 70 fs duration. The delay between the pump-probe pulses was varied between zero and 5 ps, and the pulses were focused to reach peak intensities above 10¹⁶W/cm² with an off-axis parabola. The direct pulse triggered the explosion of single aerosolised sucrose nano-particles, while the delayed pulse probed the exploding structure. The ejected ions were measured by ion time of flight spectrometry, and the particle sizes were measured by coherent diffractive imaging. The results show that sucrose particles of 560-1000 nm diameter retain their size for about 500 fs following the first exposure. Significant sample expansion happens between 500 fs and 1 ps. We present simulations to support these observations.
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Andreasson J, Martin AV, Liang M, Timneanu N, Aquila A, Wang F, Iwan B, Svenda M, Ekeberg T, Hantke M, Bielecki J, Rolles D, Rudenko A, Foucar L, Hartmann R, Erk B, Rudek B, Chapman HN, Hajdu J, Barty A. Automated identification and classification of single particle serial femtosecond X-ray diffraction data. Opt Express 2014; 22:2497-2510. [PMID: 24663542 DOI: 10.1364/oe.22.002497] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The first hard X-ray laser, the Linac Coherent Light Source (LCLS), produces 120 shots per second. Particles injected into the X-ray beam are hit randomly and in unknown orientations by the extremely intense X-ray pulses, where the femtosecond-duration X-ray pulses diffract from the sample before the particle structure is significantly changed even though the sample is ultimately destroyed by the deposited X-ray energy. Single particle X-ray diffraction experiments generate data at the FEL repetition rate, resulting in more than 400,000 detector readouts in an hour, the data stream during an experiment contains blank frames mixed with hits on single particles, clusters and contaminants. The diffraction signal is generally weak and it is superimposed on a low but continually fluctuating background signal, originating from photon noise in the beam line and electronic noise from the detector. Meanwhile, explosion of the sample creates fragments with a characteristic signature. Here, we describe methods based on rapid image analysis combined with ion Time-of-Flight (ToF) spectroscopy of the fragments to achieve an efficient, automated and unsupervised sorting of diffraction data. The studies described here form a basis for the development of real-time frame rejection methods, e.g. for the European XFEL, which is expected to produce 100 million pulses per hour.
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Ge X, Boutu W, Gauthier D, Wang F, Borta A, Barbrel B, Ducousso M, Gonzalez AI, Carré B, Guillaumet D, Perdrix M, Gobert O, Gautier J, Lambert G, Maia FRNC, Hajdu J, Zeitoun P, Merdji H. Impact of wave front and coherence optimization in coherent diffractive imaging. Opt Express 2013; 21:11441-11447. [PMID: 23670000 DOI: 10.1364/oe.21.011441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We present single shot nanoscale imaging using a table-top femtosecond soft X-ray laser harmonic source at a wavelength of 32 nm. We show that the phase retrieval process in coherent diffractive imaging critically depends on beam quality. Coherence and image fidelity are measured from single-shot coherent diffraction patterns of isolated nano-patterned slits. Impact of flux, wave front and coherence of the soft X-ray beam on the phase retrieval process and the image quality are discussed. After beam improvements, a final image reconstruction is presented with a spatial resolution of 78 nm (half period) in a single 20 fs laser harmonic shot.
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Affiliation(s)
- X Ge
- Commissariat à l’Energie Atomique, Service des Photons, Atomes et Molécules, Bâtiment 522, Centre d’Etude de Saclay, 91191 Gif-sur-Yvette, France
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Thomas H, Helal A, Hoffmann K, Kandadai N, Keto J, Andreasson J, Iwan B, Seibert M, Timneanu N, Hajdu J, Adolph M, Gorkhover T, Rupp D, Schorb S, Möller T, Doumy G, DiMauro LF, Hoener M, Murphy B, Berrah N, Messerschmidt M, Bozek J, Bostedt C, Ditmire T. Explosions of xenon clusters in ultraintense femtosecond x-ray pulses from the LCLS free electron laser. Phys Rev Lett 2012; 108:133401. [PMID: 22540697 DOI: 10.1103/physrevlett.108.133401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 10/21/2011] [Indexed: 05/31/2023]
Abstract
Explosions of large Xe clusters (<N> ~ 11,000) irradiated by femtosecond pulses of 850 eV x-ray photons focused to an intensity of up to 10(17) W/cm(2) from the Linac Coherent Light Source were investigated experimentally. Measurements of ion charge-state distributions and energy spectra exhibit strong evidence for the formation of a Xe nanoplasma in the intense x-ray pulse. This x-ray produced Xe nanoplasma is accompanied by a three-body recombination and hydrodynamic expansion. These experimental results appear to be consistent with a model in which a spherically exploding nanoplasma is formed inside the Xe cluster and where the plasma temperature is determined by photoionization heating.
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Affiliation(s)
- H Thomas
- Texas Center for High Intensity Laser Science, University of Texas, Austin, Texas 78712, USA
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Aquila A, Hunter MS, Doak RB, Kirian RA, Fromme P, White TA, Andreasson J, Arnlund D, Bajt S, Barends TRM, Barthelmess M, Bogan MJ, Bostedt C, Bottin H, Bozek JD, Caleman C, Coppola N, Davidsson J, DePonte DP, Elser V, Epp SW, Erk B, Fleckenstein H, Foucar L, Frank M, Fromme R, Graafsma H, Grotjohann I, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann R, Hau-Riege S, Hauser G, Hirsemann H, Holl P, Holton JM, Hömke A, Johansson L, Kimmel N, Kassemeyer S, Krasniqi F, Kühnel KU, Liang M, Lomb L, Malmerberg E, Marchesini S, Martin AV, Maia FRNC, Messerschmidt M, Nass K, Reich C, Neutze R, Rolles D, Rudek B, Rudenko A, Schlichting I, Schmidt C, Schmidt KE, Schulz J, Seibert MM, Shoeman RL, Sierra R, Soltau H, Starodub D, Stellato F, Stern S, Strüder L, Timneanu N, Ullrich J, Wang X, Williams GJ, Weidenspointner G, Weierstall U, Wunderer C, Barty A, Spence JCH, Chapman HN. Time-resolved protein nanocrystallography using an X-ray free-electron laser. Opt Express 2012; 20:2706-16. [PMID: 22330507 PMCID: PMC3413412 DOI: 10.1364/oe.20.002706] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 12/16/2011] [Accepted: 12/18/2011] [Indexed: 05/17/2023]
Abstract
We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
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Affiliation(s)
- Andrew Aquila
- Center for Free-Electron Laser Science, DESY, Notkestraße 85, 22607 Hamburg, Germany.
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Koopmann R, Cupelli K, Redecke L, Nass K, Deponte DP, White TA, Stellato F, Rehders D, Liang M, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Boutet S, Bozek JD, Caleman C, Coppola N, Davidsson J, Doak RB, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Holl P, Hunter MS, Kassemeyer S, Kirian RA, Lomb L, Maia FRNC, Kimmel N, Martin AV, Messerschmidt M, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert MM, Shoeman RL, Sierra RG, Soltau H, Stern S, Strüder L, Timneanu N, Ullrich J, Wang X, Weidenspointner G, Weierstall U, Williams GJ, Wunderer CB, Fromme P, Spence JCH, Stehle T, Chapman HN, Betzel C, Duszenko M. In vivo protein crystallization opens new routes in structural biology. Nat Methods 2012; 9:259-62. [PMID: 22286384 PMCID: PMC3429599 DOI: 10.1038/nmeth.1859] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 12/21/2011] [Indexed: 11/08/2022]
Abstract
Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo-grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.
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Affiliation(s)
- Rudolf Koopmann
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
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Barty A, Caleman C, Aquila A, Timneanu N, Lomb L, White TA, Andreasson J, Arnlund D, Bajt S, Barends TRM, Barthelmess M, Bogan MJ, Bostedt C, Bozek JD, Coffee R, Coppola N, Davidsson J, DePonte DP, Doak RB, Ekeberg T, Elser V, Epp SW, Erk B, Fleckenstein H, Foucar L, Fromme P, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann R, Hartmann A, Hauser G, Hirsemann H, Holl P, Hunter MS, Johansson L, Kassemeyer S, Kimmel N, Kirian RA, Liang M, Maia FRNC, Malmerberg E, Marchesini S, Martin AV, Nass K, Neutze R, Reich C, Rolles D, Rudek B, Rudenko A, Scott H, Schlichting I, Schulz J, Seibert MM, Shoeman RL, Sierra RG, Soltau H, Spence JCH, Stellato F, Stern S, Strüder L, Ullrich J, Wang X, Weidenspointner G, Weierstall U, Wunderer CB, Chapman HN. Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements. Nat Photonics 2012; 6:35-40. [PMID: 24078834 PMCID: PMC3783007 DOI: 10.1038/nphoton.2011.297] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis1. For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information1-4. Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology5 should enable structural determination from submicrometre protein crystals with atomic resolution.
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Affiliation(s)
- Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Correspondence and requests for materials should be addressed to A.B. and H.N.C., ;
| | - Carl Caleman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrew Aquila
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Lukas Lomb
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - David Arnlund
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Saša Bajt
- Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas R. M. Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Michael J. Bogan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - John D. Bozek
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Ryan Coffee
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Nicola Coppola
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jan Davidsson
- Department of Photochemistry and Molecular Science, Uppsala University, Box 523, SE-75120 Uppsala, Sweden
| | - Daniel P. DePonte
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - R. Bruce Doak
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Veit Elser
- Department of Physics, Cornell University, Ithaca, New York 14853, USA
| | - Sascha W. Epp
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Benjamin Erk
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lutz Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Heinz Graafsma
- Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lars Gumprecht
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Christina Y. Hampton
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | | | - Günter Hauser
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | | | - Peter Holl
- PN Sensor GmbH, Otto-Hahn-Ring 6, 81739 München, Germany
| | - Mark S. Hunter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Linda Johansson
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Stephan Kassemeyer
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nils Kimmel
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | - Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Mengning Liang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Erik Malmerberg
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | | | - Andrew V. Martin
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Karol Nass
- University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Richard Neutze
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | | | - Daniel Rolles
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Benedikt Rudek
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Artem Rudenko
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Howard Scott
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Joachim Schulz
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - M. Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Robert L. Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Raymond G. Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Heike Soltau
- PN Sensor GmbH, Otto-Hahn-Ring 6, 81739 München, Germany
| | - John C. H. Spence
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Francesco Stellato
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Stephan Stern
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lothar Strüder
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
| | - Joachim Ullrich
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - X. Wang
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Georg Weidenspointner
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | | | - Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Correspondence and requests for materials should be addressed to A.B. and H.N.C., ;
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44
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Yoon CH, Schwander P, Abergel C, Andersson I, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek J, Chapman HN, Claverie JM, Coppola N, DePonte DP, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann E, Hartmann R, Hauser G, Hirsemann H, Holl P, Kassemeyer S, Kimmel N, Kiskinova M, Liang M, Loh NTD, Lomb L, Maia FRNC, Martin AV, Nass K, Pedersoli E, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert M, Seltzer V, Shoeman RL, Sierra RG, Soltau H, Starodub D, Steinbrener J, Stier G, Strüder L, Svenda M, Ullrich J, Weidenspointner G, White TA, Wunderer C, Ourmazd A. Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering. Opt Express 2011; 19:16542-9. [PMID: 21935018 DOI: 10.1364/oe.19.016542] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.
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Affiliation(s)
- Chun Hong Yoon
- Department of Physics, University of Wisconsin-Milwaukee, 1900 East Kenwood Blvd, Milwaukee, Wisconsin 53211, USA
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45
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Pedersoli E, Capotondi F, Cocco D, Zangrando M, Kaulich B, Menk RH, Locatelli A, Mentes TO, Spezzani C, Sandrin G, Bacescu DM, Kiskinova M, Bajt S, Barthelmess M, Barty A, Schulz J, Gumprecht L, Chapman HN, Nelson AJ, Frank M, Pivovaroff MJ, Woods BW, Bogan MJ, Hajdu J. Multipurpose modular experimental station for the DiProI beamline of Fermi@Elettra free electron laser. Rev Sci Instrum 2011; 82:043711. [PMID: 21529017 DOI: 10.1063/1.3582155] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present a compact modular apparatus with a flexible design that will be operated at the DiProI beamline of the Fermi@Elettra free electron laser (FEL) for performing static and time-resolved coherent diffraction imaging experiments, taking advantage of the full coherence and variable polarization of the short seeded FEL pulses. The apparatus has been assembled and the potential of the experimental setup is demonstrated by commissioning tests with coherent synchrotron radiation. This multipurpose experimental station will be open to general users after installation at the Fermi@Elettra free electron laser in 2011.
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Affiliation(s)
- Emanuele Pedersoli
- Fermi, Elettra Sincrotrone Trieste, SS 14 - km 163.5, 34149 Basovizza, Trieste, Italy
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46
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Sokolowski-Tinten K, Barty A, Boutet S, Shymanovich U, Chapman H, Bogan M, Marchesini S, Hau-Riege S, Stojanovic N, Bonse J, Rosandi Y, Urbassek HM, Tobey R, Ehrke H, Cavalleri A, Düsterer S, Redlin H, Frank M, Bajt S, Schulz J, Seibert M, Hajdu J, Treusch R, Bostedt C, Hoener M, Möeller T. Short-pulse Laser Induced Transient Structure Formation and Ablation Studied with Time-resolved Coherent XUV-scattering. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-1230-mm05-03] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractThe structural dynamics of short-pulse laser irradiated surfaces and nano-structures has been studied with nm spatial and ultrafast temporal resolution by means of single-shot coherent XUV-scattering techniques. The experiments allowed us to time-resolve the formation of laser-induced periodic surface structures, and to follow the expansion and disintegration of nano-objects during laser ablation.
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47
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Caleman C, Huldt G, Maia FRNC, Ortiz C, Parak FG, Hajdu J, van der Spoel D, Chapman HN, Timneanu N. On the feasibility of nanocrystal imaging using intense and ultrashort X-ray pulses. ACS Nano 2011; 5:139-46. [PMID: 21138321 DOI: 10.1021/nn1020693] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest in the crystal. X-ray lasers offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses. Such pulses may allow the imaging of single molecules, clusters, or nanoparticles. Coherent flash imaging will also open up new avenues for structural studies on nano- and microcrystalline substances. This paper addresses the theoretical potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances and simulate the primary and secondary ionization dynamics in the crystalline sample. The results establish conditions for ultrafast single-shot nanocrystallography diffraction experiments as a function of X-ray fluence, pulse duration, and the size of nanocrystals. Nanocrystallography using ultrafast X-ray pulses has the potential to open up a new route in protein crystallography to solve atomic structures of many systems that remain inaccessible using conventional X-ray sources.
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Affiliation(s)
- Carl Caleman
- Physik Department E17, Technische Universität München, James-Franck-Strasse, DE-85748 Garching, Germany
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48
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Andreasson J, Iwan B, Andrejczuk A, Abreu E, Bergh M, Caleman C, Nelson AJ, Bajt S, Chalupsky J, Chapman HN, Fäustlin RR, Hajkova V, Heimann PA, Hjörvarsson B, Juha L, Klinger D, Krzywinski J, Nagler B, Pálsson GK, Singer W, Seibert MM, Sobierajski R, Toleikis S, Tschentscher T, Vinko SM, Lee RW, Hajdu J, Tîmneanu N. Saturated ablation in metal hydrides and acceleration of protons and deuterons to keV energies with a soft-x-ray laser. Phys Rev E Stat Nonlin Soft Matter Phys 2011; 83:016403. [PMID: 21405780 DOI: 10.1103/physreve.83.016403] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 11/25/2010] [Indexed: 05/30/2023]
Abstract
Studies of materials under extreme conditions have relevance to a broad area of research, including planetary physics, fusion research, materials science, and structural biology with x-ray lasers. We study such extreme conditions and experimentally probe the interaction between ultrashort soft x-ray pulses and solid targets (metals and their deuterides) at the FLASH free-electron laser where power densities exceeding 10(17) W/cm(2) were reached. Time-of-flight ion spectrometry and crater analysis were used to characterize the interaction. The results show the onset of saturation in the ablation process at power densities above 10(16) W/cm(2). This effect can be linked to a transiently induced x-ray transparency in the solid by the femtosecond x-ray pulse at high power densities. The measured kinetic energies of protons and deuterons ejected from the surface reach several keV and concur with predictions from plasma-expansion models. Simulations of the interactions were performed with a nonlocal thermodynamic equilibrium code with radiation transfer. These calculations return critical depths similar to the observed crater depths and capture the transient surface transparency at higher power densities.
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Affiliation(s)
- J Andreasson
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
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49
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Maia FRNC, Ekeberg T, van der Spoel D, Hajdu J. Hawk: the image reconstruction package for coherent X-ray diffractive imaging. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889810036083] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The past few years have seen a tremendous growth in the field of coherent X-ray diffractive imaging, in large part due to X-ray free-electron lasers which provide a peak brilliance billions of times higher than that of synchrotrons. However, this rapid development in terms of hardware has not been matched on the software side. The release ofHawkis intended to close this gap. To the authors' knowledgeHawkis the first publicly available and fully open source software program for reconstructing images from continuous diffraction patterns. The software handles all steps leading from a raw diffraction pattern to a reconstructed two-dimensional image including geometry determination, background correction, masking and phasing. It also includes preliminary three-dimensional support and support for graphics processing units using the Compute Unified Device Architecture, which speeds up processing by orders of magnitude compared to a single central processing unit.Hawkimplements numerous algorithms and is easily extended. This, in combination with its open-source licence, provides a platform for other groups to test, develop and distribute their own algorithms.Hawkis available under the GNU General Public License from http://xray.bmc.uu.se/hawk.
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50
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Cryan JP, Glownia JM, Andreasson J, Belkacem A, Berrah N, Blaga CI, Bostedt C, Bozek J, Buth C, DiMauro LF, Fang L, Gessner O, Guehr M, Hajdu J, Hertlein MP, Hoener M, Kornilov O, Marangos JP, March AM, McFarland BK, Merdji H, Petrović VS, Raman C, Ray D, Reis D, Tarantelli F, Trigo M, White JL, White W, Young L, Bucksbaum PH, Coffee RN. Auger electron angular distribution of double core-hole states in the molecular reference frame. Phys Rev Lett 2010; 105:083004. [PMID: 20868096 DOI: 10.1103/physrevlett.105.083004] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Indexed: 05/29/2023]
Abstract
The Linac Coherent Light Source free electron laser is a source of high brightness x rays, 2×10(11) photons in a ∼5 fs pulse, that can be focused to produce double core vacancies through rapid sequential ionization. This enables double core vacancy Auger electron spectroscopy, an entirely new way to study femtosecond chemical dynamics with Auger electrons that probe the local valence structure of molecules near a specific atomic core. Using 1.1 keV photons for sequential x-ray ionization of impulsively aligned molecular nitrogen, we observed a rich single-site double core vacancy Auger electron spectrum near 413 eV, in good agreement with ab initio calculations, and we measured the corresponding Auger electron angle dependence in the molecular frame.
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Affiliation(s)
- James P Cryan
- SLAC National Accelerator Laboratory, The PULSE Institute for Ultrafast Energy Science, 2575 Sand Hill Road, Menlo Park, California 94025, USA.
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