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Stern S, Holmegaard L, Filsinger F, Rouzée A, Rudenko A, Johnsson P, Martin AV, Barty A, Bostedt C, Bozek J, Coffee R, Epp S, Erk B, Foucar L, Hartmann R, Kimmel N, Kühnel KU, Maurer J, Messerschmidt M, Rudek B, Starodub D, Thøgersen J, Weidenspointner G, White TA, Stapelfeldt H, Rolles D, Chapman HN, Küpper J. Toward atomic resolution diffractive imaging of isolated molecules with X-ray free-electron lasers. Faraday Discuss 2015; 171:393-418. [PMID: 25415561 DOI: 10.1039/c4fd00028e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We give a detailed account of the theoretical analysis and the experimental results of an X-ray-diffraction experiment on quantum-state selected and strongly laser-aligned gas-phase ensembles of the prototypical large asymmetric rotor molecule 2,5-diiodobenzonitrile, performed at the Linac Coherent Light Source [Phys. Rev. Lett.112, 083002 (2014)]. This experiment is the first step toward coherent diffractive imaging of structures and structural dynamics of isolated molecules at atomic resolution, i.e., picometers and femtoseconds, using X-ray free-electron lasers.
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Affiliation(s)
- S Stern
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany.
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2
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Park HJ, Loh ND, Sierra RG, Hampton CY, Starodub D, Martin AV, Barty A, Aquila A, Schulz J, Steinbrener J, Shoeman RL, Lomb L, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, Tobias HJ, Farquar GR, Benner WH, Hau-Riege S, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Strueder L, Ullrich J, Bucksbaum P, Frank M, Schlichting I, Chapman HN, Bogan MJ, Elser V. Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers. Opt Express 2013; 21:28729-42. [PMID: 24514385 DOI: 10.1364/oe.21.028729] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.
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3
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Starodub D, Aquila A, Bajt S, Barthelmess M, Barty A, Bostedt C, Bozek JD, Coppola N, Doak RB, Epp SW, Erk B, Foucar L, Gumprecht L, Hampton CY, Hartmann A, Hartmann R, Holl P, Kassemeyer S, Kimmel N, Laksmono H, Liang M, Loh ND, Lomb L, Martin AV, Nass K, Reich C, Rolles D, Rudek B, Rudenko A, Schulz J, Shoeman RL, Sierra RG, Soltau H, Steinbrener J, Stellato F, Stern S, Weidenspointner G, Frank M, Ullrich J, Strüder L, Schlichting I, Chapman HN, Spence JCH, Bogan MJ. Single-particle structure determination by correlations of snapshot X-ray diffraction patterns. Nat Commun 2013; 3:1276. [PMID: 23232406 DOI: 10.1038/ncomms2288] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 11/14/2012] [Indexed: 11/09/2022] Open
Abstract
Diffractive imaging with free-electron lasers allows structure determination from ensembles of weakly scattering identical nanoparticles. The ultra-short, ultra-bright X-ray pulses provide snapshots of the randomly oriented particles frozen in time, and terminate before the onset of structural damage. As signal strength diminishes for small particles, the synthesis of a three-dimensional diffraction volume requires simultaneous involvement of all data. Here we report the first application of a three-dimensional spatial frequency correlation analysis to carry out this synthesis from noisy single-particle femtosecond X-ray diffraction patterns of nearly identical samples in random and unknown orientations, collected at the Linac Coherent Light Source. Our demonstration uses unsupported test particles created via aerosol self-assembly, and composed of two polystyrene spheres of equal diameter. The correlation analysis avoids the need for orientation determination entirely. This method may be applied to the structural determination of biological macromolecules in solution.
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Affiliation(s)
- D Starodub
- PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.
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4
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Loh ND, Starodub D, Lomb L, Hampton CY, Martin AV, Sierra RG, Barty A, Aquila A, Schulz J, Steinbrener J, Shoeman RL, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, White TA, Tobias HJ, Farquar GR, Benner WH, Hau-Riege S, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Strueder L, Ullrich J, Bucksbaum P, Frank M, Schlichting I, Chapman HN, Bogan MJ. Sensing the wavefront of x-ray free-electron lasers using aerosol spheres. Opt Express 2013; 21:12385-12394. [PMID: 23736456 DOI: 10.1364/oe.21.012385] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [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
Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 10(21) W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.
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Affiliation(s)
- N Duane Loh
- PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
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5
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Sierra RG, Laksmono H, Kern J, Tran R, Hattne J, Alonso-Mori R, Lassalle-Kaiser B, Glöckner C, Hellmich J, Schafer DW, Echols N, Gildea RJ, Grosse-Kunstleve RW, Sellberg J, McQueen TA, Fry AR, Messerschmidt MM, Miahnahri A, Seibert MM, Hampton CY, Starodub D, Loh ND, Sokaras D, Weng TC, Zwart PH, Glatzel P, Milathianaki D, White WE, Adams PD, Williams GJ, Boutet S, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK, Bogan MJ. Nanoflow electrospinning serial femtosecond crystallography. Acta Crystallogr D Biol Crystallogr 2012; 68:1584-7. [PMID: 23090408 PMCID: PMC3478121 DOI: 10.1107/s0907444912038152] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [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: 07/24/2012] [Accepted: 09/05/2012] [Indexed: 11/10/2022]
Abstract
An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14-3.1 µl min(-1) to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 µl min(-1) and diffracted to beyond 4 Å resolution, producing 14,000 indexable diffraction patterns, or four per second, from 140 µg of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption.
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Affiliation(s)
- Raymond G. Sierra
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Hartawan Laksmono
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | - Carina Glöckner
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Julia Hellmich
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Donald W. Schafer
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Richard J. Gildea
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Jonas Sellberg
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Physics, AlbaNova, Stockholm University, S-106 91 Stockholm, Sweden
| | - Trevor A. McQueen
- Department of Chemistry, Stanford University, Stanford, CA 94025, USA
| | - Alan R. Fry
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Alan Miahnahri
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - M. Marvin Seibert
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Christina Y. Hampton
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Dmitri Starodub
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - N. Duane Loh
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Tsu-Chien Weng
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Petrus H. Zwart
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pieter Glatzel
- European Synchrotron Radiation Facility, Grenoble, France
| | | | - William E. White
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Garth J. Williams
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Athina Zouni
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - Nicholas K. Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uwe Bergmann
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vittal K. Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael J. Bogan
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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6
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Loh ND, Hampton CY, Martin AV, Starodub D, Sierra RG, Barty A, Aquila A, Schulz J, Lomb L, Steinbrener J, Shoeman RL, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, White TA, Tobias HJ, Farquar GR, Benner WH, Hau-Riege SP, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Bucksbaum P, Hodgson KO, Strüder L, Ullrich J, Frank M, Schlichting I, Chapman HN, Bogan MJ. Erratum: Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight. Nature 2012. [DOI: 10.1038/nature11426] [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: 11/09/2022]
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7
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Loh ND, Hampton CY, Martin AV, Starodub D, Sierra RG, Barty A, Aquila A, Schulz J, Lomb L, Steinbrener J, Shoeman RL, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Hunter MM, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, White TA, Tobias HJ, Farquar GR, Benner WH, Hau-Riege SP, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Bucksbaum P, Hodgson KO, Strüder L, Ullrich J, Frank M, Schlichting I, Chapman HN, Bogan MJ. Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight. Nature 2012; 486:513-7. [PMID: 22739316 DOI: 10.1038/nature11222] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 05/09/2012] [Indexed: 11/09/2022]
Abstract
The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology to climate science, yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate; visible light scattering provides insufficient resolution; and X-ray synchrotron studies have been limited to ensembles of particles. Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins, vibrational energy transfer by the hydrodynamic interaction of amino acids, and large-scale production of nanoscale structures by flame synthesis.
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Affiliation(s)
- N D Loh
- PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
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8
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Martin AV, Loh ND, Hampton CY, Sierra RG, Wang F, Aquila A, Bajt S, Barthelmess M, Bostedt C, Bozek JD, Coppola N, Epp SW, Erk B, Fleckenstein H, Foucar L, Frank M, Graafsma H, Gumprecht L, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Holl P, Kassemeyer S, Kimmel N, Liang M, Lomb L, Maia FRNC, Marchesini S, Nass K, Pedersoli E, Reich C, Rolles D, Rudek B, Rudenko A, Schulz J, Shoeman RL, Soltau H, Starodub D, Steinbrener J, Stellato F, Strüder L, Ullrich J, Weidenspointner G, White TA, Wunderer CB, Barty A, Schlichting I, Bogan MJ, Chapman HN. Femtosecond dark-field imaging with an X-ray free electron laser. Opt Express 2012; 20:13501-12. [PMID: 22714377 DOI: 10.1364/oe.20.013501] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The emergence of femtosecond diffractive imaging with X-ray lasers has enabled pioneering structural studies of isolated particles, such as viruses, at nanometer length scales. However, the issue of missing low frequency data significantly limits the potential of X-ray lasers to reveal sub-nanometer details of micrometer-sized samples. We have developed a new technique of dark-field coherent diffractive imaging to simultaneously overcome the missing data issue and enable us to harness the unique contrast mechanisms available in dark-field microscopy. Images of airborne particulate matter (soot) up to two microns in length were obtained using single-shot diffraction patterns obtained at the Linac Coherent Light Source, four times the size of objects previously imaged in similar experiments. This technique opens the door to femtosecond diffractive imaging of a wide range of micrometer-sized materials that exhibit irreproducible complexity down to the nanoscale, including airborne particulate matter, small cells, bacteria and gold-labeled biological samples.
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Affiliation(s)
- A V Martin
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.
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9
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Kassemeyer S, Steinbrener J, Lomb L, Hartmann E, Aquila A, Barty A, Martin AV, Hampton CY, Bajt S, Barthelmess M, Barends TRM, Bostedt C, Bott M, Bozek JD, Coppola N, Cryle M, DePonte DP, Doak RB, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Hömke A, Holl P, Jönsson O, Kimmel N, Krasniqi F, Liang M, Maia FRNC, Marchesini S, Nass K, Reich C, Rolles D, Rudek B, Rudenko A, Schmidt C, Schulz J, Shoeman RL, Sierra RG, Soltau H, Spence JCH, Starodub D, Stellato F, Stern S, Stier G, Svenda M, Weidenspointner G, Weierstall U, White TA, Wunderer C, Frank M, Chapman HN, Ullrich J, Strüder L, Bogan MJ, Schlichting I. Femtosecond free-electron laser x-ray diffraction data sets for algorithm development. Opt Express 2012; 20:4149-58. [PMID: 22418172 DOI: 10.1364/oe.20.004149] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.
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Affiliation(s)
- Stephan Kassemeyer
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
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10
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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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11
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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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12
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Hunter MS, DePonte DP, Shapiro DA, Kirian RA, Wang X, Starodub D, Marchesini S, Weierstall U, Doak RB, Spence JCH, Fromme P. X-ray diffraction from membrane protein nanocrystals. Biophys J 2011; 100:198-206. [PMID: 21190672 DOI: 10.1016/j.bpj.2010.10.049] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 10/02/2010] [Accepted: 10/13/2010] [Indexed: 11/25/2022] Open
Abstract
Membrane proteins constitute > 30% of the proteins in an average cell, and yet the number of currently known structures of unique membrane proteins is < 300. To develop new concepts for membrane protein structure determination, we have explored the serial nanocrystallography method, in which fully hydrated protein nanocrystals are delivered to an x-ray beam within a liquid jet at room temperature. As a model system, we have collected x-ray powder diffraction data from the integral membrane protein Photosystem I, which consists of 36 subunits and 381 cofactors. Data were collected from crystals ranging in size from 100 nm to 2 μm. The results demonstrate that there are membrane protein crystals that contain < 100 unit cells (200 total molecules) and that 3D crystals of membrane proteins, which contain < 200 molecules, may be suitable for structural investigation. Serial nanocrystallography overcomes the problem of x-ray damage, which is currently one of the major limitations for x-ray structure determination of small crystals. By combining serial nanocrystallography with x-ray free-electron laser sources in the future, it may be possible to produce molecular-resolution electron-density maps using membrane protein crystals that contain only a few hundred or thousand unit cells.
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Affiliation(s)
- M S Hunter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
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Saldin DK, Shneerson VL, Starodub D, Spence JCH. Reconstruction from a single diffraction pattern of azimuthally projected electron density of molecules aligned parallel to a single axis. Acta Crystallogr A 2009; 66:32-7. [PMID: 20029131 DOI: 10.1107/s0108767309041749] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 10/12/2009] [Indexed: 11/10/2022] Open
Abstract
Diffraction from the individual molecules of a molecular beam, aligned parallel to a single axis by a strong electric field or other means, has been proposed as a means of structure determination of individual molecules. As in fiber diffraction, all the information extractable is contained in a diffraction pattern from incidence of the diffracting beam normal to the molecular alignment axis. The limited size of the object results in continuous diffraction patterns characterized by neither Bragg spots nor layer lines. Equations relating the scattered amplitudes to the molecular electron density may be conveniently formulated in terms of cylindrical harmonics. For simulated diffraction patterns from short C nanotubes aligned along their axes, iterative solution of the equation for the zeroth-order cylindrical harmonic and its inverse with appropriate constraints in real and reciprocal space enables the phasing of the measured amplitudes, and hence a reconstruction of the azimuthal projection of the molecule.
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Affiliation(s)
- D K Saldin
- Department of Physics, University of Wisconsin-Milwaukee, PO Box 413, Milwaukee, WI 53201, USA.
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14
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Ho PJ, Starodub D, Saldin DK, Shneerson VL, Ourmazd A, Santra R. Molecular structure determination from x-ray scattering patterns of laser-aligned symmetric-top molecules. J Chem Phys 2009; 131:131101. [DOI: 10.1063/1.3245404] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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15
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Howells MR, Beetz T, Chapman HN, Cui C, Holton JM, Jacobsen CJ, Kirz J, Lima E, Marchesini S, Miao H, Sayre D, Shapiro DA, Spence JCH, Starodub D. An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy. J Electron Spectros Relat Phenomena 2009; 170:4-12. [PMID: 20463854 PMCID: PMC2867487 DOI: 10.1016/j.elspec.2008.10.008] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
X-ray diffraction microscopy (XDM) is a new form of x-ray imaging that is being practiced at several third-generation synchrotron-radiation x-ray facilities. Nine years have elapsed since the technique was first introduced and it has made rapid progress in demonstrating high-resolution three-dimensional imaging and promises few-nm resolution with much larger samples than can be imaged in the transmission electron microscope. Both life- and materials-science applications of XDM are intended, and it is expected that the principal limitation to resolution will be radiation damage for life science and the coherent power of available x-ray sources for material science. In this paper we address the question of the role of radiation damage. We use a statistical analysis based on the so-called "dose fractionation theorem" of Hegerl and Hoppe to calculate the dose needed to make an image of a single life-science sample by XDM with a given resolution. We find that for simply-shaped objects the needed dose scales with the inverse fourth power of the resolution and present experimental evidence to support this finding. To determine the maximum tolerable dose we have assembled a number of data taken from the literature plus some measurements of our own which cover ranges of resolution that are not well covered otherwise. The conclusion of this study is that, based on the natural contrast between protein and water and "Rose-criterion" image quality, one should be able to image a frozen-hydrated biological sample using XDM at a resolution of about 10 nm.
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Affiliation(s)
- M. R. Howells
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - T. Beetz
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - H. N. Chapman
- Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA 94550, USA
| | - C. Cui
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - J. M. Holton
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2330, USA
| | - C. J. Jacobsen
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - J. Kirz
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - E. Lima
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - S. Marchesini
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - H. Miao
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - D. Sayre
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - D. A. Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - J. C. H. Spence
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287-1504, USA
| | - D. Starodub
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287-1504, USA
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Shapiro DA, Chapman HN, Deponte D, Doak RB, Fromme P, Hembree G, Hunter M, Marchesini S, Schmidt K, Spence J, Starodub D, Weierstall U. Powder diffraction from a continuous microjet of submicrometer protein crystals. J Synchrotron Radiat 2008; 15:593-9. [PMID: 18955765 DOI: 10.1107/s0909049508024151] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 07/29/2008] [Indexed: 05/06/2023]
Abstract
Atomic-resolution structures from small proteins have recently been determined from high-quality powder diffraction patterns using a combination of stereochemical restraints and Rietveld refinement [Von Dreele (2007), J. Appl. Cryst. 40, 133-143; Margiolaki et al. (2007), J. Am. Chem. Soc. 129, 11865-11871]. While powder diffraction data have been obtained from batch samples of small crystal-suspensions, which are exposed to X-rays for long periods of time and undergo significant radiation damage, the proof-of-concept that protein powder diffraction data from nanocrystals of a membrane protein can be obtained using a continuous microjet is shown. This flow-focusing aerojet has been developed to deliver a solution of hydrated protein nanocrystals to an X-ray beam for diffraction analysis. This method requires neither the crushing of larger polycrystalline samples nor any techniques to avoid radiation damage such as cryocooling. Apparatus to record protein powder diffraction in this manner has been commissioned, and in this paper the first powder diffraction patterns from a membrane protein, photosystem I, with crystallite sizes of less than 500 nm are presented. These preliminary patterns show the lowest-order reflections, which agree quantitatively with theoretical calculations of the powder profile. The results also serve to test our aerojet injector system, with future application to femtosecond diffraction in free-electron X-ray laser schemes, and for serial crystallography using a single-file beam of aligned hydrated molecules.
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Affiliation(s)
- D A Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Schmidt KE, Spence JCH, Weierstall U, Kirian R, Wang X, Starodub D, Chapman HN, Howells MR, Doak RB. Tomographic femtosecond x-ray diffractive imaging. Phys Rev Lett 2008; 101:115507. [PMID: 18851299 DOI: 10.1103/physrevlett.101.115507] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Indexed: 05/26/2023]
Abstract
A method is proposed for obtaining three simultaneous projections of a target from a single radiation pulse, which also allows the relative orientation of successive targets to be determined. The method has application to femtosecond x-ray diffraction, and does not require solution of the phase problem. We show that the principal axes of a compact charge-density distribution can be obtained from projections of its autocorrelation function, which is directly accessible in diffraction experiments. The results may have more general application to time resolved tomographic pump-probe experiments and time-series imaging.
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Affiliation(s)
- K E Schmidt
- Department of Physics, Arizona State University, Tempe, Arizona 85287-1504, USA
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18
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Weierstall U, Spence J, Starodub D, Schmidt K, Doak R, Shapiro D, Chapman H, Marchesini S. Diffractive imaging and serial crystallography. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308095834] [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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19
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Starodub D, Rez P, Hembree G, Howells M, Shapiro D, Chapman HN, Fromme P, Schmidt K, Weierstall U, Doak RB, Spence JCH. Dose, exposure time and resolution in serial X-ray crystallography. J Synchrotron Radiat 2008; 15:62-73. [PMID: 18097080 DOI: 10.1107/s0909049507048893] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 10/05/2007] [Indexed: 05/25/2023]
Abstract
The resolution of X-ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed serial crystallography method, the damage problem is addressed by distributing the total dose over many identical hydrated macromolecules running continuously in a single-file train across a continuous X-ray beam, and resolution is then limited only by the available molecular and X-ray fluxes and molecular alignment. Orientation of the diffracting molecules is achieved by laser alignment. The incident X-ray fluence (energy/area) is evaluated that is required to obtain a given resolution from (i) an analytical model, giving the count rate at the maximum scattering angle for a model protein, (ii) explicit simulation of diffraction patterns for a GroEL-GroES protein complex, and (iii) the spatial frequency cut-off of the transfer function following iterative solution of the phase problem, and reconstruction of an electron density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate counting time and the number of proteins needed within the beam at any instant for a given resolution and X-ray flux. An inverse fourth-power dependence of exposure time on resolution is confirmed, with important implications for all coherent X-ray imaging. It is found that multiple single-file protein beams will be needed for sub-nanometer resolution on current third-generation synchrotrons, but not on fourth-generation designs, where reconstruction of secondary protein structure at a resolution of 7 A should be possible with relatively short exposures.
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Affiliation(s)
- D Starodub
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA.
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Starodub D, Doak RB, Schmidt K, Weierstall U, Wu JS, Spence JCH, Howells M, Marcus M, Shapiro D, Barty A, Chapman HN. Damped and thermal motion of laser-aligned hydrated macromolecule beams for diffraction. J Chem Phys 2005; 123:244304. [PMID: 16396534 DOI: 10.1063/1.2137313] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We consider a monodispersed Rayleigh droplet beam of water droplets doped with proteins. An intense infrared laser is used to align these droplets. The arrangement has been proposed for electron- and x-ray-diffraction studies of proteins which are difficult to crystallize. This paper considers the effect of thermal fluctuations on the angular spread of alignment in thermal equilibrium, and relaxation phenomena, particularly the damping of oscillations excited as the molecules enter the field. The possibility of adiabatic alignment is also considered. We find that damping times in a high-pressure gas cell as used in x-ray-diffraction experiments are short compared with the time taken for molecules to traverse the beam and that a suitably shaped field might be used for electron-diffraction experiments in vacuum to provide adiabatic alignment, thus obviating the need for a damping gas cell.
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Affiliation(s)
- D Starodub
- Department of Physics and Astronomy, Arizona State University, P.O. Box 871504 Tempe, Arizona 85287-1504, USA.
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Weierstall U, Starodub D, Spence JCH, Doak B. Electron diffraction from a beam of laser-aligned proteins: progress report. Acta Crystallogr A 2005. [DOI: 10.1107/s010876730509625x] [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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22
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Spence JC, Doak B, Weierstall U, Schmidt K, Fromme P, Starodub D, Wu J, Hembree G, Howells M, Shapiro D, Chapman H. Diffraction from a laser-aligned beam of hydrated proteins. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305095103] [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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