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Thorne RE. Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization. Acta Crystallogr D Struct Biol 2023; 79:78-94. [PMID: 36601809 PMCID: PMC9815097 DOI: 10.1107/s2059798322011652] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/04/2022] [Indexed: 01/05/2023] Open
Abstract
For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein-solvent glass transition near 200 K to ∼350 K. Fischer has recently reviewed practical methods for room-temperature data collection and analysis [Fischer (2021), Q. Rev. Biophys. 54, e1]. Here, the key advantages and physical principles of, and methods for, crystallographic data collection at noncryogenic temperatures and some factors relevant to interpreting the resulting data are discussed. For room-temperature data collection to realize its potential within the structural biology toolkit, streamlined and standardized methods for delivering crystals prepared in the home laboratory to the synchrotron and for automated handling and data collection, similar to those for cryocrystallography, should be implemented.
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Affiliation(s)
- Robert E. Thorne
- Physics Department, Cornell University, Ithaca, NY 14853, USA
- MiTeGen LLC, PO Box 3867, Ithaca, NY 14850, USA
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Giewekemeyer K, Aquila A, Loh NTD, Chushkin Y, Shanks KS, Weiss J, Tate MW, Philipp HT, Stern S, Vagovic P, Mehrjoo M, Teo C, Barthelmess M, Zontone F, Chang C, Tiberio RC, Sakdinawat A, Williams GJ, Gruner SM, Mancuso AP. Experimental 3D coherent diffractive imaging from photon-sparse random projections. IUCRJ 2019; 6:357-365. [PMID: 31098017 PMCID: PMC6503918 DOI: 10.1107/s2052252519002781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/24/2019] [Indexed: 05/19/2023]
Abstract
The routine atomic resolution structure determination of single particles is expected to have profound implications for probing structure-function relationships in systems ranging from energy-storage materials to biological molecules. Extremely bright ultrashort-pulse X-ray sources - X-ray free-electron lasers (XFELs) - provide X-rays that can be used to probe ensembles of nearly identical nanoscale particles. When combined with coherent diffractive imaging, these objects can be imaged; however, as the resolution of the images approaches the atomic scale, the measured data are increasingly difficult to obtain and, during an X-ray pulse, the number of photons incident on the 2D detector is much smaller than the number of pixels. This latter concern, the signal 'sparsity', materially impedes the application of the method. An experimental analog using a conventional X-ray source is demonstrated and yields signal levels comparable with those expected from single biomolecules illuminated by focused XFEL pulses. The analog experiment provides an invaluable cross check on the fidelity of the reconstructed data that is not available during XFEL experiments. Using these experimental data, it is established that a sparsity of order 1.3 × 10-3 photons per pixel per frame can be overcome, lending vital insight to the solution of the atomic resolution XFEL single-particle imaging problem by experimentally demonstrating 3D coherent diffractive imaging from photon-sparse random projections.
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Affiliation(s)
| | - A. Aquila
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - N.-T. D. Loh
- Centre for Bio-imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117551 Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore
| | - Y. Chushkin
- ESRF – The European Synchrotron, 71 avenue des Martyrs, 38000 Grenoble, France
| | - K. S. Shanks
- Laboratory for Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - J.T. Weiss
- Laboratory for Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - M. W. Tate
- Laboratory for Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - H. T. Philipp
- Laboratory for Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - S. Stern
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - P. Vagovic
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - M. Mehrjoo
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - C. Teo
- Centre for Bio-imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore
| | - M. Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - F. Zontone
- ESRF – The European Synchrotron, 71 avenue des Martyrs, 38000 Grenoble, France
| | - C. Chang
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - R. C. Tiberio
- Stanford Nano Shared Facilities, Stanford University, 348 Via Pueblo, Stanford, CA 94305, USA
| | - A. Sakdinawat
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - G. J. Williams
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - S. M. Gruner
- Laboratory for Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA
| | - A. P. Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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Lan TY, Wierman JL, Tate MW, Philipp HT, Martin-Garcia JM, Zhu L, Kissick D, Fromme P, Fischetti RF, Liu W, Elser V, Gruner SM. Solving protein structure from sparse serial microcrystal diffraction data at a storage-ring synchrotron source. IUCRJ 2018; 5:548-558. [PMID: 30224958 PMCID: PMC6126656 DOI: 10.1107/s205225251800903x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/20/2018] [Indexed: 05/29/2023]
Abstract
In recent years, the success of serial femtosecond crystallography and the paucity of beamtime at X-ray free-electron lasers have motivated the development of serial microcrystallography experiments at storage-ring synchrotron sources. However, especially at storage-ring sources, if a crystal is too small it will have suffered significant radiation damage before diffracting a sufficient number of X-rays into Bragg peaks for peak-indexing software to determine the crystal orientation. As a consequence, the data frames of small crystals often cannot be indexed and are discarded. Introduced here is a method based on the expand-maximize-compress (EMC) algorithm to solve protein structures, specifically from data frames for which indexing methods fail because too few X-rays are diffracted into Bragg peaks. The method is demonstrated on a real serial microcrystallography data set whose signals are too weak to be indexed by conventional methods. In spite of the daunting background scatter from the sample-delivery medium, it was still possible to solve the protein structure at 2.1 Å resolution. The ability of the EMC algorithm to analyze weak data frames will help to reduce sample consumption. It will also allow serial microcrystallography to be performed with crystals that are otherwise too small to be feasibly analyzed at storage-ring sources.
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Affiliation(s)
- Ti-Yen Lan
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - Jennifer L. Wierman
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Macromolecular Diffraction Facility at CHESS (MacCHESS), Cornell University, Ithaca, NY 14853, USA
| | - Mark W. Tate
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - Hugh T. Philipp
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - Jose M. Martin-Garcia
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Lan Zhu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - David Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Robert F. Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Wei Liu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Veit Elser
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - Sol M. Gruner
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Macromolecular Diffraction Facility at CHESS (MacCHESS), Cornell University, Ithaca, NY 14853, USA
- Kavli Institute for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA
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Lan TY, Wierman JL, Tate MW, Philipp HT, Elser V, Gruner SM. Reconstructing three-dimensional protein crystal intensities from sparse unoriented two-axis X-ray diffraction patterns. Corrigendum. J Appl Crystallogr 2018; 51:230. [PMID: 29507552 PMCID: PMC5822995 DOI: 10.1107/s1600576718000171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 12/16/2017] [Indexed: 11/24/2022] Open
Abstract
Corrigendum to J. Appl. Cryst. (2017), 50, 985–993. A figure in the article by Lan, Wierman, Tate, Philipp, Elser & Gruner [J. Appl. Cryst. (2017), 50, 985–993] is corrected.
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