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Eom I, Chun SH, Lee JH, Nam D, Ma R, Park J, Park S, Park SH, Yang H, Nam I, Cho MH, Shim CH, Kim G, Min C, Heo H, Kang H, Kim C. Recent Progress of the PAL-XFEL. Applied Sciences 2022; 12:1010. [DOI: 10.3390/app12031010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The X-ray free-electron laser of the Pohang Accelerator Laboratory (PAL-XFEL) was opened to users in 2017. Since then, significant progress has been made in PAL-XFEL operation and beamline experiments. This includes increasing the FEL pulse energy, increasing the FEL photon energy, generating self-seeding FEL, and trials of two-color operation. In the beamline, new instruments or endstations have been added or are being prepared. Overall, beamline operation has been stabilized since its initiation, which has enabled excellent scientific results through efficient user experiments. In this paper, we describe details of the recent progress of the PAL-XFEL.
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2
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Chang YP, Yin Z, Balciunas T, Wörner HJ, Wolf JP. Temperature measurements of liquid flat jets in vacuum. Struct Dyn 2022; 9:014901. [PMID: 35224132 PMCID: PMC8853733 DOI: 10.1063/4.0000139] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Sub-μm thin samples are essential for spectroscopic purposes. The development of flat micro-jets enabled novel spectroscopic and scattering methods for investigating molecular systems in the liquid phase. However, the temperature of these ultra-thin liquid sheets in vacuum has not been systematically investigated. Here, we present a comprehensive temperature characterization using optical Raman spectroscopy of sub-micron flatjets produced by two different methods: colliding of two cylindrical jets and a cylindrical jet compressed by a high pressure gas. Our results reveal the dependence of the cooling rate on the material properties and the source characteristics, i.e., nozzle-orifice size, flow rate, and pressure. We show that materials with higher vapor pressures exhibit faster cooling rates, which is illustrated by comparing the temperature profiles of water and ethanol flatjets. In a sub-μm liquid sheet, the temperature of the water sample reaches around 268 K and the ethanol around 253 K close to the flatjet's terminus.
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Affiliation(s)
- Yi-Ping Chang
- GAP-Biophotonics, Université de Genève, 1205 Geneva, Switzerland
| | - Zhong Yin
- Laboratorium für Physikalische Chemie, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Hans Jakob Wörner
- Laboratorium für Physikalische Chemie, ETH Zürich, 8093 Zürich, Switzerland
| | - Jean-Pierre Wolf
- GAP-Biophotonics, Université de Genève, 1205 Geneva, Switzerland
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3
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Lahey-Rudolph JM, Schönherr R, Barthelmess M, Fischer P, Seuring C, Wagner A, Meents A, Redecke L. Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals. IUCrJ 2021; 8:665-677. [PMID: 34258014 PMCID: PMC8256716 DOI: 10.1107/s2052252521005297] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/18/2021] [Indexed: 05/05/2023]
Abstract
The crystallization of recombinant proteins in living cells is an exciting new approach in structural biology. Recent success has highlighted the need for fast and efficient diffraction data collection, optimally directly exposing intact crystal-containing cells to the X-ray beam, thus protecting the in cellulo crystals from environmental challenges. Serial femtosecond crystallography (SFX) at free-electron lasers (XFELs) allows the collection of detectable diffraction even from tiny protein crystals, but requires very fast sample exchange to utilize each XFEL pulse. Here, an efficient approach is presented for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micometre-sized crystals of the protein HEX-1 from the fungus Neurospora crassa on a fixed target. Employing the fast and highly accurate Roadrunner II translation-stage system allowed efficient raster scanning of the pores of micro-patterned, single-crystalline silicon chips loaded with living, crystal-containing insect cells. Compared with liquid-jet and LCP injection systems, the increased hit rates of up to 30% and reduced background scattering enabled elucidation of the HEX-1 structure. Using diffraction data from only a single chip collected within 12 min at the Linac Coherent Light Source, a 1.8 Å resolution structure was obtained with significantly reduced sample consumption compared with previous SFX experiments using liquid-jet injection. This HEX-1 structure is almost superimposable with that previously determined using synchrotron radiation from single HEX-1 crystals grown by sitting-drop vapour diffusion, validating the approach. This study demonstrates that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection using living, crystal-containing cells, and offers huge potential for the straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources.
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Affiliation(s)
- J. Mia Lahey-Rudolph
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Carolin Seuring
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, 22671 Hamburg, Germany
| | - Armin Wagner
- Diamond Light Source, Diamond House DH2-52, Chilton, Didcot OX11 0DE, United Kingdom
| | - Alke Meents
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
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4
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de Kock MB, Azim S, Kassier GH, Miller RJD. Determining the radial distribution function of water using electron scattering: A key to solution phase chemistry. J Chem Phys 2020; 153:194504. [DOI: 10.1063/5.0024127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. B. de Kock
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Bldg. 99 (CFEL), 22761 Hamburg, Germany
| | - S. Azim
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Bldg. 99 (CFEL), 22761 Hamburg, Germany
| | - G. H. Kassier
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Bldg. 99 (CFEL), 22761 Hamburg, Germany
| | - R. J. D. Miller
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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5
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Orville AM. Recent results in time resolved serial femtosecond crystallography at XFELs. Curr Opin Struct Biol 2020; 65:193-208. [PMID: 33049498 DOI: 10.1016/j.sbi.2020.08.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/24/2020] [Accepted: 08/30/2020] [Indexed: 11/30/2022]
Abstract
Time-resolved serial femtosecond crystallography (tr-SFX) methods exploit slurries of crystalline samples that range in size from hundreds of nanometers to a few tens of micrometers, at near-physiological temperature and pressure, to generate atomic resolution models and probe authentic function with the same experiment. 'Dynamic structural biology' is often used to encompass the research philosophy and techniques. Reaction cycles for tr-SFX studies are initiated by photons or ligand addition/mixing strategies, wherein the latter are potentially generalizable across enzymology. Thus, dynamic structural biology often creates stop-motion molecular movies of macromolecular function. In metal-dependent systems, complementary spectroscopic information can also be collected from the same samples and X-ray pulses, which provides even more detailed mechanistic insights. These types of experimental data also complement quantum mechanical and classical dynamics numerical calculations. Correlated structural-functional results will yield more detailed mechanistic insights and will likely translate into better drugs and treatments impacting human health, and better catalysis for clean energy and agriculture.
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Affiliation(s)
- Allen M Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom; Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, United Kingdom.
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6
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Lee D, Park S, Lee K, Kim J, Park G, Nam KH, Baek S, Chung WK, Lee JL, Cho Y, Park J. Application of a high-throughput microcrystal delivery system to serial femtosecond crystallography. J Appl Crystallogr 2020; 53:477-485. [PMID: 32280322 PMCID: PMC7133064 DOI: 10.1107/s1600576720002423] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 10/17/2019] [Accepted: 02/20/2020] [Indexed: 01/26/2023] Open
Abstract
Microcrystal delivery methods are pivotal in the use of serial femtosecond crystallography (SFX) to resolve the macromolecular structures of proteins. Here, the development of a novel technique and instruments for efficiently delivering microcrystals for SFX are presented. The new method, which relies on a one-dimensional fixed-target system that includes a microcrystal container, consumes an extremely low amount of sample compared with conventional two-dimensional fixed-target techniques at ambient temperature. This novel system can deliver soluble microcrystals without highly viscous carrier media and, moreover, can be used as a microcrystal growth device for SFX. Diffraction data collection utilizing this advanced technique along with a real-time visual servo scan system has been successfully demonstrated for the structure determination of proteinase K microcrystals at 1.85 Å resolution.
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Affiliation(s)
- Donghyeon Lee
- Department of Mechanical Engineering, POSTECH, 77 Cheongam-Ro, Pohang, 37673, Republic of Korea
| | - Sehan Park
- PAL-XFEL, Pohang Accelerator Laboratory, 80 Jigok-ro 127 beongil, Pohang, 37673, Republic of Korea
| | - Keondo Lee
- Department of Mechanical Engineering, POSTECH, 77 Cheongam-Ro, Pohang, 37673, Republic of Korea
| | - Jangwoo Kim
- PAL-XFEL, Pohang Accelerator Laboratory, 80 Jigok-ro 127 beongil, Pohang, 37673, Republic of Korea
| | - Gisu Park
- PAL-XFEL, Pohang Accelerator Laboratory, 80 Jigok-ro 127 beongil, Pohang, 37673, Republic of Korea
| | - Ki Hyun Nam
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seoul, 02841, Republic of Korea.,Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seoul, 02841, Republic of Korea
| | - Sangwon Baek
- Department of Materials Science and Engineering, POSTECH, 77 Cheongam-Ro, Pohang, 37673, Republic of Korea
| | - Wan Kyun Chung
- Department of Mechanical Engineering, POSTECH, 77 Cheongam-Ro, Pohang, 37673, Republic of Korea
| | - Jong-Lam Lee
- Department of Materials Science and Engineering, POSTECH, 77 Cheongam-Ro, Pohang, 37673, Republic of Korea
| | - Yunje Cho
- Department of Life Sciences, POSTECH, 77 Cheongam-Ro, Pohang, 37673, Republic of Korea
| | - Jaehyun Park
- PAL-XFEL, Pohang Accelerator Laboratory, 80 Jigok-ro 127 beongil, Pohang, 37673, Republic of Korea
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7
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Nunes JPF, Ledbetter K, Lin M, Kozina M, DePonte DP, Biasin E, Centurion M, Crissman CJ, Dunning M, Guillet S, Jobe K, Liu Y, Mo M, Shen X, Sublett R, Weathersby S, Yoneda C, Wolf TJA, Yang J, Cordones AA, Wang XJ. Liquid-phase mega-electron-volt ultrafast electron diffraction. Struct Dyn 2020; 7:024301. [PMID: 32161776 PMCID: PMC7062553 DOI: 10.1063/1.5144518] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 02/13/2020] [Indexed: 05/23/2023]
Abstract
The conversion of light into usable chemical and mechanical energy is pivotal to several biological and chemical processes, many of which occur in solution. To understand the structure-function relationships mediating these processes, a technique with high spatial and temporal resolutions is required. Here, we report on the design and commissioning of a liquid-phase mega-electron-volt (MeV) ultrafast electron diffraction instrument for the study of structural dynamics in solution. Limitations posed by the shallow penetration depth of electrons and the resulting information loss due to multiple scattering and the technical challenge of delivering liquids to vacuum were overcome through the use of MeV electrons and a gas-accelerated thin liquid sheet jet. To demonstrate the capabilities of this instrument, the structure of water and its network were resolved up to the 3 rd hydration shell with a spatial resolution of 0.6 Å; preliminary time-resolved experiments demonstrated a temporal resolution of 200 fs.
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Affiliation(s)
- J P F Nunes
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | | | - M Lin
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - M Kozina
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - D P DePonte
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - E Biasin
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - M Centurion
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - C J Crissman
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
| | - M Dunning
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - S Guillet
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - K Jobe
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Y Liu
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, USA
| | - M Mo
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - X Shen
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - R Sublett
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - S Weathersby
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - C Yoneda
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - T J A Wolf
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | | | - A A Cordones
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - X J Wang
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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8
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Abstract
X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.
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Affiliation(s)
- Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
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9
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Smeets S, Zou X, Wan W. Serial electron crystallography for structure determination and phase analysis of nanocrystalline materials. J Appl Crystallogr 2018; 51:1262-1273. [PMID: 30279637 PMCID: PMC6157704 DOI: 10.1107/s1600576718009500] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 04/16/2018] [Accepted: 07/03/2018] [Indexed: 11/16/2022] Open
Abstract
Serial electron crystallography has been developed as a fully automated method to collect diffraction data on polycrystalline materials using a transmission electron microscope. This enables useful data to be collected on materials that are sensitive to the electron beam and thus difficult to measure using the conventional methods that require long exposure of the same crystal. The data collection strategy combines goniometer translation with electron beam shift, which allows the entire sample stage to be probed. At each position of the goniometer, the locations of the crystals are identified using image recognition techniques. Diffraction data are then collected on each crystal using a quasi-parallel focused beam with a predefined size (usually 300-500 nm). It is shown that with a fast and sensitive Timepix hybrid pixel area detector it is possible to collect diffraction data of up to 3500 crystals per hour. These data can be indexed using a brute-force forward-projection algorithm. Results from several test samples show that 100-200 frames are enough for structure determination using direct methods or dual-space methods. The large number of crystals examined enables quantitative phase analysis and automatic screening of materials for known and unknown phases.
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Affiliation(s)
- Stef Smeets
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-106, Sweden
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-106, Sweden
| | - Wei Wan
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-106, Sweden
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10
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Park J, Kim S, Kim S, Nam KH. Multifarious injection chamber for molecular structure study (MICOSS) system: development and application for serial femtosecond crystallography at Pohang Accelerator Laboratory X-ray Free-Electron Laser. J Synchrotron Radiat 2018; 25:323-328. [PMID: 29488909 DOI: 10.1107/s160057751800022x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/04/2018] [Indexed: 06/08/2023]
Abstract
The multifarious injection chamber for molecular structure study (MICOSS) experimental system has been developed at the Pohang Accelerator Laboratory X-ray Free-Electron Laser for conducting serial femtosecond crystallography. This system comprises several instruments such as a dedicated sample chamber, sample injectors, sample environment diagnostic system and detector stage for convenient distance manipulation. Serial femtosecond crystallography experiments of lysozyme crystals have been conducted successfully. The diffraction peaks have reached to ∼1.8 Å resolution at the photon energy of 9.785 keV.
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Affiliation(s)
- Jaehyun Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Seonghan Kim
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sangsoo Kim
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Ki Hyun Nam
- Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
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11
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Selikhanov GK, Fando MS, Dontsova MV, Gabdulkhakov AG. Investigations of Photosensitive Proteins by Serial Crystallography. Biochemistry Moscow 2018; 83:S163-S175. [DOI: 10.1134/s0006297918140134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Nelson G, Kirian RA, Weierstall U, Zatsepin NA, Faragó T, Baumbach T, Wilde F, Niesler FBP, Zimmer B, Ishigami I, Hikita M, Bajt S, Yeh SR, Rousseau DL, Chapman HN, Spence JCH, Heymann M. Three-dimensional-printed gas dynamic virtual nozzles for x-ray laser sample delivery. Opt Express 2016; 24:11515-30. [PMID: 27410079 PMCID: PMC5025224 DOI: 10.1364/oe.24.011515] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Reliable sample delivery is essential to biological imaging using X-ray Free Electron Lasers (XFELs). Continuous injection using the Gas Dynamic Virtual Nozzle (GDVN) has proven valuable, particularly for time-resolved studies. However, many important aspects of GDVN functionality have yet to be thoroughly understood and/or refined due to fabrication limitations. We report the application of 2-photon polymerization as a form of high-resolution 3D printing to fabricate high-fidelity GDVNs with submicron resolution. This technique allows rapid prototyping of a wide range of different types of nozzles from standard CAD drawings and optimization of crucial dimensions for optimal performance. Three nozzles were tested with pure water to determine general nozzle performance and reproducibility, with nearly reproducible off-axis jetting being the result. X-ray tomography and index matching were successfully used to evaluate the interior nozzle structures and identify the cause of off-axis jetting. Subsequent refinements to fabrication resulted in straight jetting. A performance test of printed nozzles at an XFEL provided high quality femtosecond diffraction patterns.
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Affiliation(s)
- Garrett Nelson
- Department of Physics, Arizona State University, Tempe, Arizona 85287,
USA
| | - Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, Arizona 85287,
USA
- Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg,
Germany
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, Arizona 85287,
USA
| | - Nadia A. Zatsepin
- Department of Physics, Arizona State University, Tempe, Arizona 85287,
USA
| | - Tomáš Faragó
- Synchrotron Facility ANKA, Karlsruhe Institute of Technology KIT, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein- Leopoldshafen,
Germany
| | - Tilo Baumbach
- Synchrotron Facility ANKA, Karlsruhe Institute of Technology KIT, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein- Leopoldshafen,
Germany
| | - Fabian Wilde
- Helmholtz-Zentrum Geesthacht, Max-Planck-Straße 1, 21502 Geesthacht,
Germany
| | - Fabian B. P. Niesler
- Nanoscribe GmbH, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen,
Germany
| | - Benjamin Zimmer
- Nanoscribe GmbH, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen,
Germany
| | - Izumi Ishigami
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461,
USA
| | - Masahide Hikita
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461,
USA
| | - Saša Bajt
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg,
Germany
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461,
USA
| | - Denis L. Rousseau
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461,
USA
| | - Henry N. Chapman
- Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg,
Germany
| | - John C. H. Spence
- Department of Physics, Arizona State University, Tempe, Arizona 85287,
USA
| | - Michael Heymann
- Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg,
Germany
- present address: Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried,
Germany
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14
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Tono K, Nango E, Sugahara M, Song C, Park J, Tanaka T, Tanaka R, Joti Y, Kameshima T, Ono S, Hatsui T, Mizohata E, Suzuki M, Shimamura T, Tanaka Y, Iwata S, Yabashi M. Diverse application platform for hard X-ray diffraction in SACLA (DAPHNIS): application to serial protein crystallography using an X-ray free-electron laser. J Synchrotron Radiat 2015; 22:532-7. [PMID: 25931065 PMCID: PMC4817517 DOI: 10.1107/s1600577515004464] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/03/2015] [Indexed: 05/06/2023]
Abstract
An experimental system for serial femtosecond crystallography using an X-ray free-electron laser (XFEL) has been developed. It basically consists of a sample chamber, fluid injectors and a two-dimensional detector. The chamber and the injectors are operated under helium atmosphere at 1 atm. The ambient pressure operation facilitates applications to fluid samples. Three kinds of injectors are employed to feed randomly oriented crystals in aqueous solution or highly viscous fluid. Experiments on lysozyme crystals were performed by using the 10 keV XFEL of the SPring-8 Angstrom Compact free-electron LAser (SACLA). The structure of model protein lysozyme from 1 µm crystals at a resolution of 2.4 Å was obtained.
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Affiliation(s)
- Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5198, Japan
- Correspondence e-mail:
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | | | - Changyong Song
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | - Jaehyun Park
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5198, Japan
| | - Takashi Kameshima
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5198, Japan
| | - Shun Ono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | - Takaki Hatsui
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mamoru Suzuki
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tatsuro Shimamura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshiki Tanaka
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5148, Japan
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15
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Abstract
AbstractThe diffract-before-destroy method, using 50- to 100-fs x-ray pulses from a free-electron laser, was designed to determine the three-dimensional structure of biological macromolecules in close to their natural state. Here we explore the possibility of using short electron pulses for the same purpose and the related question of whether radiation damage can be outrun with electrons. Major problems include Coulomb repulsion within the incident beam and the need for high lateral coherence, difficulties that are discussed in terms of existing and future electron sources. Using longer pulses of electrons appears to make the attainment of near-atomic resolution more feasible, at least for nanocrystalline particles, whereas obtaining this information from single-molecule particles in an aqueous environment seems a more distant goal. We also consider the possibility of serial crystallography using a liquid jet injector with a continuous electron beam in a transmission electron microscope (TEM).
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16
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Abstract
X-ray free-electron lasers overcome the problem of radiation damage in protein crystallography and allow structure determination from micro- and nanocrystals at room temperature. To ensure that consecutive X-ray pulses do not probe previously exposed crystals, the sample needs to be replaced with the X-ray repetition rate, which ranges from 120 Hz at warm linac-based free-electron lasers to 1 MHz at superconducting linacs. Liquid injectors are therefore an essential part of a serial femtosecond crystallography experiment at an X-ray free-electron laser. Here, we compare different techniques of injecting microcrystals in solution into the pulsed X-ray beam in vacuum. Sample waste due to mismatch of the liquid flow rate to the X-ray repetition rate can be addressed through various techniques.
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Affiliation(s)
- Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
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17
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Marmiroli B, Cacho-Nerin F, Sartori B, Pérez J, Amenitsch H. Thorough small-angle X-ray scattering analysis of the instability of liquid micro-jets in air. J Synchrotron Radiat 2014; 21:193-202. [PMID: 24365936 DOI: 10.1107/s1600577513027951] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/11/2013] [Indexed: 06/03/2023]
Abstract
Liquid jets are of interest, both for their industrial relevance and for scientific applications (more important, in particular for X-rays, after the advent of free-electron lasers that require liquid jets as sample carrier). Instability mechanisms have been described theoretically and by numerical simulation, but confirmed by few experimental techniques. In fact, these are mainly based on cameras, which is limited by the imaging resolution, and on light scattering, which is hindered by absorption, reflection, Mie scattering and multiple scattering due to complex air/liquid interfaces during jet break-up. In this communication it is demonstrated that synchrotron small-angle X-ray scattering (SAXS) can give quantitative information on liquid jet dynamics at the nanoscale, by detecting time-dependent morphology and break-up length. Jets ejected from circular tubes of different diameters (100-450 µm) and speeds (0.7-21 m s(-1)) have been explored to cover the Rayleigh and first wind-induced regimes. Various solvents (water, ethanol, 2-propanol) and their mixtures have been examined. The determination of the liquid jet behaviour becomes essential, as it provides background data in subsequent studies of chemical and biological reactions using SAXS or X-ray diffraction based on synchrotron radiation and free-electron lasers.
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Affiliation(s)
- Benedetta Marmiroli
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, Graz 8010, Austria
| | - Fernando Cacho-Nerin
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, Graz 8010, Austria
| | - Barbara Sartori
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, Graz 8010, Austria
| | - Javier Pérez
- Beamline SWING, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif sur Yvette, France
| | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, Graz 8010, Austria
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18
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Randolph SJ, Botman A, Toth M. Capsule-free fluid delivery and beam-induced electrodeposition in a scanning electron microscope. RSC Adv 2013. [DOI: 10.1039/c3ra42840k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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19
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Abstract
Research opportunities and techniques are reviewed for the application of hard x-ray pulsed free-electron lasers (XFEL) to structural biology. These include the imaging of protein nanocrystals, single particles such as viruses, pump--probe experiments for time-resolved nanocrystallography, and snapshot wide-angle x-ray scattering (WAXS) from molecules in solution. The use of femtosecond exposure times, rather than freezing of samples, as a means of minimizing radiation damage is shown to open up new opportunities for the molecular imaging of biochemical reactions at room temperature in solution. This is possible using a 'diffract-and-destroy' mode in which the incident pulse terminates before radiation damage begins. Methods for delivering hundreds of hydrated bioparticles per second (in random orientations) to a pulsed x-ray beam are described. New data analysis approaches are outlined for the correlated fluctuations in fast WAXS, for protein nanocrystals just a few molecules on a side, and for the continuous x-ray scattering from a single virus. Methods for determining the orientation of a molecule from its diffraction pattern are reviewed. Methods for the preparation of protein nanocrystals are also reviewed. New opportunities for solving the phase problem for XFEL data are outlined. A summary of the latest results is given, which now extend to atomic resolution for nanocrystals. Possibilities for time-resolved chemistry using fast WAXS (solution scattering) from mixtures is reviewed, toward the general goal of making molecular movies of biochemical processes.
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Affiliation(s)
- J C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
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20
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Fromme P, Spence JCH. Femtosecond nanocrystallography using X-ray lasers for membrane protein structure determination. Curr Opin Struct Biol 2011; 21:509-16. [PMID: 21752635 DOI: 10.1016/j.sbi.2011.06.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 06/08/2011] [Indexed: 10/18/2022]
Abstract
The invention of free electron X-ray lasers has opened a new era for membrane protein structure determination with the recent first proof-of-principle of the new concept of femtosecond nanocrystallography. Structure determination is based on thousands of diffraction snapshots that are collected on a fully hydrated stream of nanocrystals. This review provides a summary of the method and describes how femtosecond X-ray crystallography overcomes the radiation-damage problem in X-ray crystallography, avoids the need for growth and freezing of large single crystals while offering a new method for direct digital phase determination by making use of the fully coherent nature of the X-ray beam. We briefly review the possibilities for time-resolved crystallography, and the potential for making 'molecular movies' of membrane proteins at work.
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Affiliation(s)
- Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA.
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