1
|
Malla TN, Zielinski K, Aldama L, Bajt S, Feliz D, Hayes B, Hunter M, Kupitz C, Lisova S, Knoska J, Martin-Garcia JM, Mariani V, Pandey S, Poudyal I, Sierra RG, Tolstikova A, Yefanov O, Yoon CH, Ourmazd A, Fromme P, Schwander P, Barty A, Chapman HN, Stojkovic EA, Batyuk A, Boutet S, Phillips GN, Pollack L, Schmidt M. Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam. Nat Commun 2023; 14:5507. [PMID: 37679343 PMCID: PMC10485065 DOI: 10.1038/s41467-023-41246-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/27/2023] [Indexed: 09/09/2023] Open
Abstract
For decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals. Here, we report in atomic detail (between 2.2 and 2.7 Å resolution) by room-temperature, time-resolved crystallography with millisecond time-resolution (with timepoints between 3 ms and 700 ms) how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating, cooperativity, induced fit, and conformational selection all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme noncovalently before reacting to a trans-enamine. This was made possible in part by the application of singular value decomposition to the MISC data using a program that remains functional even if unit cell parameters change up to 3 Å during the reaction.
Collapse
Affiliation(s)
- Tek Narsingh Malla
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Kara Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Luis Aldama
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Sasa Bajt
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Denisse Feliz
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Brendon Hayes
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark Hunter
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christopher Kupitz
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Stella Lisova
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Juraj Knoska
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Jose Manuel Martin-Garcia
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain
| | - Valerio Mariani
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ishwor Poudyal
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Raymond G Sierra
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Chung Hong Yoon
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Abbas Ourmazd
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, 20 Arizona State University, Tempe, AZ, USA
| | - Peter Schwander
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Anton Barty
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Center for Data and Computing in Natural Science CDCS, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Emina A Stojkovic
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Alexander Batyuk
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
| |
Collapse
|
2
|
Young ID, Mendez D, Poon BK, Blaschke JP, Wittwer F, Wall ME, Sauter NK. Interpreting macromolecular diffraction through simulation. Methods Enzymol 2023; 688:195-222. [PMID: 37748827 DOI: 10.1016/bs.mie.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
This chapter discusses the use of diffraction simulators to improve experimental outcomes in macromolecular crystallography, in particular for future experiments aimed at diffuse scattering. Consequential decisions for upcoming data collection include the selection of either a synchrotron or free electron laser X-ray source, rotation geometry or serial crystallography, and fiber-coupled area detector technology vs. pixel-array detectors. The hope is that simulators will provide insights to make these choices with greater confidence. Simulation software, especially those packages focused on physics-based calculation of the diffraction, can help to predict the location, size, shape, and profile of Bragg spots and diffuse patterns in terms of an underlying physical model, including assumptions about the crystal's mosaic structure, and therefore can point to potential issues with data analysis in the early planning stages. Also, once the data are collected, simulation may offer a pathway to improve the measurement of diffraction, especially with weak data, and might help to treat problematic cases such as overlapping patterns.
Collapse
Affiliation(s)
- Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Derek Mendez
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, United States
| | - Billy K Poon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Johannes P Blaschke
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Felix Wittwer
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Michael E Wall
- Computer, Computational and Statistical Sciences Division, Los Alamos, NM, United States
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
| |
Collapse
|
3
|
Keown JR, Crawshaw AD, Trincao J, Carrique L, Gildea RJ, Horrell S, Warren AJ, Axford D, Owen R, Evans G, Bézier A, Metcalf P, Grimes JM. Atomic structure of a nudivirus occlusion body protein determined from a 70-year-old crystal sample. Nat Commun 2023; 14:4160. [PMID: 37443157 PMCID: PMC10345106 DOI: 10.1038/s41467-023-39819-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Infectious protein crystals are an essential part of the viral lifecycle for double-stranded DNA Baculoviridae and double-stranded RNA cypoviruses. These viral protein crystals, termed occlusion bodies or polyhedra, are dense protein assemblies that form a crystalline array, encasing newly formed virions. Here, using X-ray crystallography we determine the structure of a polyhedrin from Nudiviridae. This double-stranded DNA virus family is a sister-group to the baculoviruses, whose members were thought to lack occlusion bodies. The 70-year-old sample contains a well-ordered lattice formed by a predominantly α-helical building block that assembles into a dense, highly interconnected protein crystal. The lattice is maintained by extensive hydrophobic and electrostatic interactions, disulfide bonds, and domain switching. The resulting lattice is resistant to most environmental stresses. Comparison of this structure to baculovirus or cypovirus polyhedra shows a distinct protein structure, crystal space group, and unit cell dimensions, however, all polyhedra utilise common principles of occlusion body assembly.
Collapse
Affiliation(s)
- Jeremy R Keown
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Adam D Crawshaw
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Jose Trincao
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Loïc Carrique
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Richard J Gildea
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Sam Horrell
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Anna J Warren
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Danny Axford
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Robin Owen
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
- Rosalind Franklin Institute, Harwell Campus, Didcot, UK
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR7261 CNRS-Université de Tours, Tours, France
| | - Peter Metcalf
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| |
Collapse
|
4
|
Agirre J, Atanasova M, Bagdonas H, Ballard CB, Baslé A, Beilsten-Edmands J, Borges RJ, Brown DG, Burgos-Mármol JJ, Berrisford JM, Bond PS, Caballero I, Catapano L, Chojnowski G, Cook AG, Cowtan KD, Croll TI, Debreczeni JÉ, Devenish NE, Dodson EJ, Drevon TR, Emsley P, Evans G, Evans PR, Fando M, Foadi J, Fuentes-Montero L, Garman EF, Gerstel M, Gildea RJ, Hatti K, Hekkelman ML, Heuser P, Hoh SW, Hough MA, Jenkins HT, Jiménez E, Joosten RP, Keegan RM, Keep N, Krissinel EB, Kolenko P, Kovalevskiy O, Lamzin VS, Lawson DM, Lebedev AA, Leslie AGW, Lohkamp B, Long F, Malý M, McCoy AJ, McNicholas SJ, Medina A, Millán C, Murray JW, Murshudov GN, Nicholls RA, Noble MEM, Oeffner R, Pannu NS, Parkhurst JM, Pearce N, Pereira J, Perrakis A, Powell HR, Read RJ, Rigden DJ, Rochira W, Sammito M, Sánchez Rodríguez F, Sheldrick GM, Shelley KL, Simkovic F, Simpkin AJ, Skubak P, Sobolev E, Steiner RA, Stevenson K, Tews I, Thomas JMH, Thorn A, Valls JT, Uski V, Usón I, Vagin A, Velankar S, Vollmar M, Walden H, Waterman D, Wilson KS, Winn MD, Winter G, Wojdyr M, Yamashita K. The CCP4 suite: integrative software for macromolecular crystallography. Acta Crystallogr D Struct Biol 2023; 79:449-461. [PMID: 37259835 PMCID: PMC10233625 DOI: 10.1107/s2059798323003595] [Citation(s) in RCA: 128] [Impact Index Per Article: 128.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/19/2023] [Indexed: 06/02/2023] Open
Abstract
The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
Collapse
Affiliation(s)
- Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Mihaela Atanasova
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Haroldas Bagdonas
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Charles B. Ballard
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - James Beilsten-Edmands
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Rafael J. Borges
- The Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - David G. Brown
- Laboratoires Servier SAS Institut de Recherches, Croissy-sur-Seine, France
| | - J. Javier Burgos-Mármol
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - John M. Berrisford
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Paul S. Bond
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Iracema Caballero
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Lucrezia Catapano
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
| | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Atlanta G. Cook
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King’s Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Kevin D. Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Tristan I. Croll
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
- Altos Labs, Portway Building, Granta Park, Great Abington, Cambridge CB21 6GP, United Kingdom
| | - Judit É. Debreczeni
- Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Nicholas E. Devenish
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Eleanor J. Dodson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Tarik R. Drevon
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Gwyndaf Evans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0QS, United Kingdom
| | - Phil R. Evans
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Maria Fando
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - James Foadi
- Department of Mathematical Sciences, University of Bath, Bath, United Kingdom
| | - Luis Fuentes-Montero
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, United Kingdom
| | - Markus Gerstel
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Richard J. Gildea
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Kaushik Hatti
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Maarten L. Hekkelman
- Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Philipp Heuser
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Soon Wen Hoh
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Michael A. Hough
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Robbie P. Joosten
- Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ronan M. Keegan
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Nicholas Keep
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Eugene B. Krissinel
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Petr Kolenko
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, 115 19 Prague 1, Czech Republic
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 55, 252 50 Vestec, Czech Republic
| | - Oleg Kovalevskiy
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Victor S. Lamzin
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - David M. Lawson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Andrey A. Lebedev
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Andrew G. W. Leslie
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Bernhard Lohkamp
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Fei Long
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Martin Malý
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, 115 19 Prague 1, Czech Republic
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 55, 252 50 Vestec, Czech Republic
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Airlie J. McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Stuart J. McNicholas
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Claudia Millán
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - James W. Murray
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robert A. Nicholls
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Martin E. M. Noble
- Translational and Clinical Research Institute, Newcastle University, Paul O’Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Robert Oeffner
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Navraj S. Pannu
- Department of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - James M. Parkhurst
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0QS, United Kingdom
| | - Nicholas Pearce
- Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden
| | - Joana Pereira
- Biozentrum and SIB Swiss Institute of Bioinformatics, University of Basel, 4056 Basel, Switzerland
| | - Anastassis Perrakis
- Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Harold R. Powell
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - William Rochira
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Massimo Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
- Discovery Centre, Biologics Engineering, AstraZeneca, Biomedical Campus, 1 Francis Crick Avenue, Trumpington, Cambridge CB2 0AA, United Kingdom
| | - Filomeno Sánchez Rodríguez
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - George M. Sheldrick
- Department of Structural Chemistry, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
| | - Kathryn L. Shelley
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Felix Simkovic
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Adam J. Simpkin
- Laboratoires Servier SAS Institut de Recherches, Croissy-sur-Seine, France
| | - Pavol Skubak
- Department of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Egor Sobolev
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Roberto A. Steiner
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
- Department of Biomedical Sciences, University of Padova, Italy
| | - Kyle Stevenson
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Ivo Tews
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Jens M. H. Thomas
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Andrea Thorn
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, 22761 Hamburg, Germany
| | - Josep Triviño Valls
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Ville Uski
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Alexei Vagin
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Melanie Vollmar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Helen Walden
- School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - David Waterman
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Martyn D. Winn
- Scientific Computing Department, Science and Technology Facilities Council, Didcot OX11 0FA, United Kingdom
| | - Graeme Winter
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Marcin Wojdyr
- Global Phasing Limited (United Kingdom), Sheraton House, Castle Park, Cambridge CB3 0AX, United Kingdom
| | - Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| |
Collapse
|
5
|
Brehm W, White T, Chapman HN. Crystal diffraction prediction and partiality estimation using Gaussian basis functions. Acta Crystallogr A Found Adv 2023; 79:145-162. [PMID: 36862040 PMCID: PMC9979942 DOI: 10.1107/s2053273323000682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023] Open
Abstract
The recent diversification of macromolecular crystallographic experiments including the use of pink beams, convergent electron diffraction and serial snapshot crystallography has shown the limitations of using the Laue equations for diffraction prediction. This article gives a computationally efficient way of calculating approximate crystal diffraction patterns given varying distributions of the incoming beam, crystal shapes and other potentially hidden parameters. This approach models each pixel of a diffraction pattern and improves data processing of integrated peak intensities by enabling the correction of partially recorded reflections. The fundamental idea is to express the distributions as weighted sums of Gaussian functions. The approach is demonstrated on serial femtosecond crystallography data sets, showing a significant decrease in the required number of patterns to refine a structure to a given error.
Collapse
Affiliation(s)
- Wolfgang Brehm
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany,Correspondence e-mail: ,
| | - Thomas White
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany,Correspondence e-mail: ,
| |
Collapse
|
6
|
Barends TR, Stauch B, Cherezov V, Schlichting I. Serial femtosecond crystallography. NATURE REVIEWS. METHODS PRIMERS 2022; 2:59. [PMID: 36643971 PMCID: PMC9833121 DOI: 10.1038/s43586-022-00141-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
With the advent of X-ray Free Electron Lasers (XFELs), new, high-throughput serial crystallography techniques for macromolecular structure determination have emerged. Serial femtosecond crystallography (SFX) and related methods provide possibilities beyond canonical, single-crystal rotation crystallography by mitigating radiation damage and allowing time-resolved studies with unprecedented temporal resolution. This primer aims to assist structural biology groups with little or no experience in serial crystallography planning and carrying out a successful SFX experiment. It discusses the background of serial crystallography and its possibilities. Microcrystal growth and characterization methods are discussed, alongside techniques for sample delivery and data processing. Moreover, it gives practical tips for preparing an experiment, what to consider and do during a beamtime and how to conduct the final data analysis. Finally, the Primer looks at various applications of SFX, including structure determination of membrane proteins, investigation of radiation damage-prone systems and time-resolved studies.
Collapse
Affiliation(s)
- Thomas R.M. Barends
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Benjamin Stauch
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Vadim Cherezov
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Ilme Schlichting
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany,
| |
Collapse
|
7
|
Casadei CM, Hosseinizadeh A, Schertler GFX, Ourmazd A, Santra R. Dynamics retrieval from stochastically weighted incomplete data by low-pass spectral analysis. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:044101. [PMID: 35991704 PMCID: PMC9385225 DOI: 10.1063/4.0000156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/12/2022] [Indexed: 05/30/2023]
Abstract
Time-resolved serial femtosecond crystallography (TR-SFX) provides access to protein dynamics on sub-picosecond timescales, and with atomic resolution. Due to the nature of the experiment, these datasets are often highly incomplete and the measured diffracted intensities are affected by partiality. To tackle these issues, one established procedure is that of splitting the data into time bins, and averaging the multiple measurements of equivalent reflections within each bin. This binning and averaging often involve a loss of information. Here, we propose an alternative approach, which we call low-pass spectral analysis (LPSA). In this method, the data are projected onto the subspace defined by a set of trigonometric functions, with frequencies up to a certain cutoff. This approach attenuates undesirable high-frequency features and facilitates retrieving the underlying dynamics. A time-lagged embedding step can be included prior to subspace projection to improve the stability of the results with respect to the parameters involved. Subsequent modal decomposition allows to produce a low-rank description of the system's evolution. Using a synthetic time-evolving model with incomplete and partial observations, we analyze the LPSA results in terms of quality of the retrieved signal, as a function of the parameters involved. We compare the performance of LPSA to that of a range of other sophisticated data analysis techniques. We show that LPSA allows to achieve excellent dynamics reconstruction at modest computational cost. Finally, we demonstrate the superiority of dynamics retrieval by LPSA compared to time binning and merging, which is, to date, the most commonly used method to extract dynamical information from TR-SFX data.
Collapse
Affiliation(s)
| | | | | | - Abbas Ourmazd
- University of Wisconsin Milwaukee, Milwaukee, Wisconsin 53201, USA
| | - Robin Santra
- Authors to whom correspondence should be addressed: and
| |
Collapse
|
8
|
Nass K, Bacellar C, Cirelli C, Dworkowski F, Gevorkov Y, James D, Johnson PJM, Kekilli D, Knopp G, Martiel I, Ozerov D, Tolstikova A, Vera L, Weinert T, Yefanov O, Standfuss J, Reiche S, Milne CJ. Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser. IUCRJ 2021; 8:905-920. [PMID: 34804544 PMCID: PMC8562661 DOI: 10.1107/s2052252521008046] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/05/2021] [Indexed: 05/25/2023]
Abstract
Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables essentially radiation-damage-free macromolecular structure determination using microcrystals that are too small for synchrotron studies. However, SFX experiments often require large amounts of sample in order to collect highly redundant data where some of the many stochastic errors can be averaged out to determine accurate structure-factor amplitudes. In this work, the capability of the Swiss X-ray free-electron laser (SwissFEL) was used to generate large-bandwidth X-ray pulses [Δλ/λ = 2.2% full width at half-maximum (FWHM)], which were applied in SFX with the aim of improving the partiality of Bragg spots and thus decreasing sample consumption while maintaining the data quality. Sensitive data-quality indicators such as anomalous signal from native thaumatin micro-crystals and de novo phasing results were used to quantify the benefits of using pink X-ray pulses to obtain accurate structure-factor amplitudes. Compared with data measured using the same setup but using X-ray pulses with typical quasi-monochromatic XFEL bandwidth (Δλ/λ = 0.17% FWHM), up to fourfold reduction in the number of indexed diffraction patterns required to obtain similar data quality was achieved. This novel approach, pink-beam SFX, facilitates the yet underutilized de novo structure determination of challenging proteins at XFELs, thereby opening the door to more scientific breakthroughs.
Collapse
Affiliation(s)
- Karol Nass
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Camila Bacellar
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Claudio Cirelli
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Florian Dworkowski
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Daniel James
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | | | - Demet Kekilli
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Gregor Knopp
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Isabelle Martiel
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Dmitry Ozerov
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Laura Vera
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Tobias Weinert
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Jörg Standfuss
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Sven Reiche
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | | |
Collapse
|
9
|
Nakane T. Pink beam crystallography demonstrated in SFX. IUCRJ 2021; 8:853-854. [PMID: 34804537 PMCID: PMC8562664 DOI: 10.1107/s2052252521010794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nass et al. [IUCrJ (2021), 8, 905-920] applied a wide bandwidth beam (pink beam) to serial femtosecond crystallography at X-ray free electron lasers. This approach will lead to better datasets in a shorter time from fewer crystals.
Collapse
Affiliation(s)
- Takanori Nakane
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| |
Collapse
|
10
|
Gorel A, Schlichting I, Barends TRM. Discerning best practices in XFEL-based biological crystallography - standards for nonstandard experiments. IUCRJ 2021; 8:532-543. [PMID: 34258002 PMCID: PMC8256713 DOI: 10.1107/s205225252100467x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/03/2021] [Indexed: 06/13/2023]
Abstract
Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) is a novel tool in structural biology. In contrast to conventional crystallography, SFX relies on merging partial intensities acquired with X-ray beams of often randomly fluctuating properties from a very large number of still diffraction images of generally randomly oriented microcrystals. For this reason, and possibly due to limitations of the still evolving data-analysis programs, XFEL-derived SFX data are typically of a lower quality than 'standard' crystallographic data. In contrast with this, the studies performed at XFELs often aim to investigate issues that require precise high-resolution data, for example to determine structures of intermediates at low occupancy, which often display very small conformational changes. This is a potentially dangerous combination and underscores the need for a critical evaluation of procedures including data-quality standards in XFEL-based structural biology. Here, such concerns are addressed.
Collapse
Affiliation(s)
- Alexander Gorel
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstr. 29, Heidelberg, 69120, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstr. 29, Heidelberg, 69120, Germany
| | - Thomas R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstr. 29, Heidelberg, 69120, Germany
| |
Collapse
|
11
|
Membrane protein crystallography in the era of modern structural biology. Biochem Soc Trans 2020; 48:2505-2524. [DOI: 10.1042/bst20200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.
Collapse
|
12
|
Nass K, Cheng R, Vera L, Mozzanica A, Redford S, Ozerov D, Basu S, James D, Knopp G, Cirelli C, Martiel I, Casadei C, Weinert T, Nogly P, Skopintsev P, Usov I, Leonarski F, Geng T, Rappas M, Doré AS, Cooke R, Nasrollahi Shirazi S, Dworkowski F, Sharpe M, Olieric N, Bacellar C, Bohinc R, Steinmetz MO, Schertler G, Abela R, Patthey L, Schmitt B, Hennig M, Standfuss J, Wang M, Milne CJ. Advances in long-wavelength native phasing at X-ray free-electron lasers. IUCRJ 2020; 7:965-975. [PMID: 33209311 PMCID: PMC7642782 DOI: 10.1107/s2052252520011379] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/19/2020] [Indexed: 05/31/2023]
Abstract
Long-wavelength pulses from the Swiss X-ray free-electron laser (XFEL) have been used for de novo protein structure determination by native single-wavelength anomalous diffraction (native-SAD) phasing of serial femtosecond crystallography (SFX) data. In this work, sensitive anomalous data-quality indicators and model proteins were used to quantify improvements in native-SAD at XFELs such as utilization of longer wavelengths, careful experimental geometry optimization, and better post-refinement and partiality correction. Compared with studies using shorter wavelengths at other XFELs and older software versions, up to one order of magnitude reduction in the required number of indexed images for native-SAD was achieved, hence lowering sample consumption and beam-time requirements significantly. Improved data quality and higher anomalous signal facilitate so-far underutilized de novo structure determination of challenging proteins at XFELs. Improvements presented in this work can be used in other types of SFX experiments that require accurate measurements of weak signals, for example time-resolved studies.
Collapse
Affiliation(s)
- Karol Nass
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Robert Cheng
- LeadXpro AG, Park InnovAARE, Villigen, 5234, Switzerland
| | - Laura Vera
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Aldo Mozzanica
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Sophie Redford
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Dmitry Ozerov
- Science IT, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Shibom Basu
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Daniel James
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Gregor Knopp
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Claudio Cirelli
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Isabelle Martiel
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Cecilia Casadei
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, Zürich, 8093, Switzerland
| | - Petr Skopintsev
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, Zürich, 8093, Switzerland
| | - Ivan Usov
- Science IT, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Filip Leonarski
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Tian Geng
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Mathieu Rappas
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Andrew S. Doré
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Robert Cooke
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | | | - Florian Dworkowski
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - May Sharpe
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Natacha Olieric
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Camila Bacellar
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Rok Bohinc
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Michel O. Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
- Biozentrum, University of Basel, Basel, 4056, Switzerland
| | - Gebhard Schertler
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, Zürich, 8093, Switzerland
| | - Rafael Abela
- LeadXpro AG, Park InnovAARE, Villigen, 5234, Switzerland
| | - Luc Patthey
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Bernd Schmitt
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Michael Hennig
- LeadXpro AG, Park InnovAARE, Villigen, 5234, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Meitian Wang
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| | - Christopher J. Milne
- Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland
| |
Collapse
|
13
|
EM-detwin: A Program for Resolving Indexing Ambiguity in Serial Crystallography Using the Expectation-Maximization Algorithm. CRYSTALS 2020. [DOI: 10.3390/cryst10070588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Serial crystallography (SX), first used as an application of X-ray free-electron lasers (XFELs), is becoming a useful method to determine atomic-resolution structures of proteins from micrometer-sized crystals with bright X-ray sources. Because of unknown orientations of crystals in SX, indexing ambiguity issue arises when the symmetry of Bravais lattice is higher than the space group symmetry, making some diffraction signals wrongly merged to the total intensity in twinned orientations. In this research, we developed a program within the CrystFEL framework, the EM-detwin, to resolve this indexing ambiguity problem based on the expectation-maximization algorithm. Testing results on the performance of the EM-detwin have demonstrated its usefulness in correctly indexing diffraction data as a valuable tool for SX data analysis.
Collapse
|
14
|
Sauter NK, Kern J, Yano J, Holton JM. Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction. Acta Crystallogr D Struct Biol 2020; 76:176-192. [PMID: 32038048 PMCID: PMC7008510 DOI: 10.1107/s2059798320000418] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/14/2020] [Indexed: 12/25/2022] Open
Abstract
Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2-3 × 10-4 (ΔE/E). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (ΔE/E = 3 × 10-3) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.
Collapse
Affiliation(s)
- Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James M. Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
15
|
Stander N, Fromme P, Zatsepin N. DatView: a graphical user interface for visualizing and querying large data sets in serial femtosecond crystallography. J Appl Crystallogr 2019; 52:1440-1448. [PMID: 31798364 PMCID: PMC6878877 DOI: 10.1107/s1600576719012044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/30/2019] [Indexed: 11/30/2022] Open
Abstract
DatView is a new graphical user interface (GUI) for plotting parameters to explore correlations, identify outliers and export subsets of data. It was designed to simplify and expedite analysis of very large unmerged serial femtosecond crystallography (SFX) data sets composed of indexing results from hundreds of thousands of microcrystal diffraction patterns. However, DatView works with any tabulated data, offering its functionality to many applications outside serial crystallography. In DatView's user-friendly GUI, selections are drawn onto plots and synchronized across all other plots, so correlations between multiple parameters in large multi-parameter data sets can be rapidly identified. It also includes an item viewer for displaying images in the current selection alongside the associated metadata. For serial crystallography data processed by indexamajig from CrystFEL [White, Kirian, Martin, Aquila, Nass, Barty & Chapman (2012 ▸). J. Appl. Cryst. 45, 335-341], DatView generates a table of parameters and metadata from stream files and, optionally, the associated HDF5 files. By combining the functionality of several commonly needed tools for SFX in a single GUI that operates on tabulated data, the time needed to load and calculate statistics from large data sets is reduced. This paper describes how DatView facilitates (i) efficient feedback during data collection by examining trends in time, sample position or any parameter, (ii) determination of optimal indexing and integration parameters via the comparison mode, (iii) identification of systematic errors in unmerged SFX data sets, and (iv) sorting and highly flexible data filtering (plot selections, Boolean filters and more), including direct export of subset CrystFEL stream files for further processing.
Collapse
Affiliation(s)
- Natasha Stander
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Nadia Zatsepin
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| |
Collapse
|
16
|
Brewster AS, Bhowmick A, Bolotovsky R, Mendez D, Zwart PH, Sauter NK. SAD phasing of XFEL data depends critically on the error model. Acta Crystallogr D Struct Biol 2019; 75:959-968. [PMID: 31692470 PMCID: PMC6834081 DOI: 10.1107/s2059798319012877] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/17/2019] [Indexed: 11/11/2022] Open
Abstract
A nonlinear least-squares method for refining a parametric expression describing the estimated errors of reflection intensities in serial crystallographic (SX) data is presented. This approach, which is similar to that used in the rotation method of crystallographic data collection at synchrotrons, propagates error estimates from photon-counting statistics to the merged data. Here, it is demonstrated that the application of this approach to SX data provides better SAD phasing ability, enabling the autobuilding of a protein structure that had previously failed to be built. Estimating the error in the merged reflection intensities requires the understanding and propagation of all of the sources of error arising from the measurements. One type of error, which is well understood, is the counting error introduced when the detector counts X-ray photons. Thus, if other types of random errors (such as readout noise) as well as uncertainties in systematic corrections (such as from X-ray attenuation) are completely understood, they can be propagated along with the counting error, as appropriate. In practice, most software packages propagate as much error as they know how to model and then include error-adjustment terms that scale the error estimates until they explain the variance among the measurements. If this is performed carefully, then during SAD phasing likelihood-based approaches can make optimal use of these error estimates, increasing the chance of a successful structure solution. In serial crystallography, SAD phasing has remained challenging, with the few examples of de novo protein structure solution each requiring many thousands of diffraction patterns. Here, the effects of different methods of treating the error estimates are estimated and it is shown that using a parametric approach that includes terms proportional to the known experimental uncertainty, the reflection intensity and the squared reflection intensity to improve the error estimates can allow SAD phasing even from weak zinc anomalous signal.
Collapse
Affiliation(s)
- Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert Bolotovsky
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Derek Mendez
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Petrus H. Zwart
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| |
Collapse
|
17
|
Khakurel KP, Angelov B, Andreasson J. Macromolecular Nanocrystal Structural Analysis with Electron and X-Rays: A Comparative Review. Molecules 2019; 24:E3490. [PMID: 31561479 PMCID: PMC6804143 DOI: 10.3390/molecules24193490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 01/10/2023] Open
Abstract
Crystallography has long been the unrivaled method that can provide the atomistic structural models of macromolecules, using either X-rays or electrons as probes. The methodology has gone through several revolutionary periods, driven by the development of new sources, detectors, and other instrumentation. Novel sources of both X-ray and electrons are constantly emerging. The increase in brightness of these sources, complemented by the advanced detection techniques, has relaxed the traditionally strict need for large, high quality, crystals. Recent reports suggest high-quality diffraction datasets from crystals as small as a few hundreds of nanometers can be routinely obtained. This has resulted in the genesis of a new field of macromolecular nanocrystal crystallography. Here we will make a brief comparative review of this growing field focusing on the use of X-rays and electrons sources.
Collapse
Affiliation(s)
- Krishna P Khakurel
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
| | - Borislav Angelov
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
| | - Jakob Andreasson
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
- Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
| |
Collapse
|
18
|
van Thor JJ. Advances and opportunities in ultrafast X-ray crystallography and ultrafast structural optical crystallography of nuclear and electronic protein dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:050901. [PMID: 31559317 PMCID: PMC6759419 DOI: 10.1063/1.5110685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/29/2019] [Indexed: 05/02/2023]
Abstract
Both nuclear and electronic dynamics contribute to protein function and need multiple and complementary techniques to reveal their ultrafast structural dynamics response. Real-space information obtained from the measurement of electron density dynamics by X-ray crystallography provides aspects of both, while the molecular physics of coherence parameters and frequency-frequency correlation needs spectroscopy methods. Ultrafast pump-probe applications of protein dynamics in crystals provide real-space information through direct X-ray crystallographic structure analysis or through structural optical crystallographic analysis. A discussion of methods of analysis using ultrafast macromolecular X-ray crystallography and ultrafast nonlinear structural optical crystallography is presented. The current and future high repetition rate capabilities provided by X-ray free electron lasers for ultrafast diffraction studies provide opportunities for optical control and optical selection of nuclear coherence which may develop to access higher frequency dynamics through improvements of sensitivity and time resolution to reveal coherence directly. Specific selection of electronic coherence requires optical probes, which can provide real-space structural information through photoselection of oriented samples and specifically in birefringent crystals. Ultrafast structural optical crystallography of photosynthetic energy transfer has been demonstrated, and the theory of two-dimensional structural optical crystallography has shown a method for accessing the structural selection of electronic coherence.
Collapse
Affiliation(s)
- Jasper J. van Thor
- Molecular Biophysics, Imperial College London, London SW7 2AZ, United Kingdom
| |
Collapse
|
19
|
Zatsepin NA, Li C, Colasurd P, Nannenga BL. The complementarity of serial femtosecond crystallography and MicroED for structure determination from microcrystals. Curr Opin Struct Biol 2019; 58:286-293. [PMID: 31345629 DOI: 10.1016/j.sbi.2019.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 11/19/2022]
Abstract
In recent years, nano and microcrystals have emerged as a valuable source of high-resolution structural information owing to the invention of serial femtosecond crystallography (SFX) with X-ray free electron lasers and microcrystal electron diffraction (MicroED) using electron cryomicroscopes. Once considered useless for structure determination, nano/microcrystals now confer significant advantages for static and time-resolved structure determination from a wide variety of difficult-to-study targets. MicroED has been used to obtain sub-Ångstrom resolution maps in which hydrogen atoms can be clearly resolved from only a few nano/microcrystals, while SFX has been used to probe protein dynamics following reaction initiation on time scales from femtoseconds to minutes. We review these two complementary techniques and their abilities for high-resolution structure determination.
Collapse
Affiliation(s)
- Nadia A Zatsepin
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, AZ 85287, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, AZ 85287, USA
| | - Paige Colasurd
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA.
| |
Collapse
|
20
|
Mishin A, Gusach A, Luginina A, Marin E, Borshchevskiy V, Cherezov V. An outlook on using serial femtosecond crystallography in drug discovery. Expert Opin Drug Discov 2019; 14:933-945. [PMID: 31184514 DOI: 10.1080/17460441.2019.1626822] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction: X-ray crystallography has made important contributions to modern drug development but its application to many important drug targets has been extremely challenging. The recent emergence of X-ray free electron lasers (XFELs) and advancements in serial femtosecond crystallography (SFX) have offered new opportunities to overcome limitations of traditional crystallography to accelerate the structure-based drug discovery (SBDD) process. Areas covered: In this review, the authors describe the general principles of X-ray generation and the main properties of XFEL beams, outline details of SFX data collection and processing, and summarize the progress in the development of associated instrumentation for sample delivery and X-ray detection. An overview of the SFX applications to various important drug targets such as membrane proteins is also provided. Expert opinion: While SFX has already made clear advancements toward the understanding of the structure and dynamics of several major drug targets, its robust application in SBDD still needs further developments of new high-throughput techniques for sample production, automation of crystal delivery and data collection, as well as for processing and storage of large amounts of data. The expansion of the available XFEL beamtime is a key to the success of SFX in SBDD.
Collapse
Affiliation(s)
- Alexey Mishin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Anastasiia Gusach
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Aleksandra Luginina
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Egor Marin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Valentin Borshchevskiy
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Vadim Cherezov
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia.,b Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California , Los Angeles , CA , USA
| |
Collapse
|
21
|
Uervirojnangkoorn M, Lyubimov AY, Zhou Q, Weis WI, Brunger AT. Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns. Acta Crystallogr D Struct Biol 2019; 75:234-241. [PMID: 30821711 PMCID: PMC6400252 DOI: 10.1107/s2059798318013177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/17/2018] [Indexed: 11/23/2022] Open
Abstract
Processing X-ray free-electron laser (XFEL) diffraction images poses challenges, as an XFEL pulse is powerful enough to destroy or damage the diffracting volume and thereby yields only one diffraction image per volume. Moreover, the crystal is stationary during the femtosecond pulse, so reflections are generally only partially recorded. Therefore, each XFEL diffraction image must be scaled individually and, ideally, corrected for partiality prior to merging. An additional complication may arise owing to indexing ambiguities when the symmetry of the Bravais lattice is higher than that of the space group, or when the unit-cell dimensions are similar to each other. Here, an automated method is presented that diagnoses these indexing ambiguities based on the Brehm-Diederichs algorithm [Brehm & Diederichs (2014), Acta Cryst. D70, 101-109] and produces a consistent indexing choice for the large majority of diffraction images. This method was applied to an XFEL diffraction data set measured from crystals of the neuronal SNARE-complexin-1-synaptotagmin-1 complex. After correcting the indexing ambiguities, substantial improvements were observed in the merging statistics and the atomic model refinement R values. This method should be a useful addition to the arsenal of tools for the processing of XFEL diffraction data sets.
Collapse
Affiliation(s)
| | - Artem Y. Lyubimov
- Stanford Synchrotron Radiation Laboratory, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - William I. Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
| | - Axel T. Brunger
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Stanford Synchrotron Radiation Laboratory, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
22
|
White TA. Processing serial crystallography data with CrystFEL: a step-by-step guide. Acta Crystallogr D Struct Biol 2019; 75:219-233. [PMID: 30821710 PMCID: PMC6400257 DOI: 10.1107/s205979831801238x] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/31/2018] [Indexed: 11/11/2022] Open
Abstract
This article provides a step-by-step guide to the use of the CrystFEL software for processing serial crystallography data from an X-ray free-electron laser or a synchrotron light source. Whereas previous papers have described the theory and algorithms and their rationale, this paper describes the steps to be performed from a user perspective, including command-line examples.
Collapse
Affiliation(s)
- Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, Germany
| |
Collapse
|
23
|
Li C, Li X, Kirian R, Spence JCH, Liu H, Zatsepin NA. SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data. IUCRJ 2019; 6:72-84. [PMID: 30713705 PMCID: PMC6327178 DOI: 10.1107/s2052252518014951] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 10/22/2018] [Indexed: 06/09/2023]
Abstract
SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns ('stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008 ▸), Acta Cryst. E64, o1286], which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL [White et al. (2012 ▸), J. Appl. Cryst. 45, 335-341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2 and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.
Collapse
Affiliation(s)
- Chufeng Li
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Xuanxuan Li
- Complex Systems Division, Beijing Computational Science Research Center, Beijing, 100193, People’s Republic of China
- Department of Engineering Physics, Tsinghua University, Beijing, 100086, People’s Republic of China
| | - Richard Kirian
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - John C. H. Spence
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, Beijing, 100193, People’s Republic of China
| | - Nadia A. Zatsepin
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| |
Collapse
|
24
|
Duyvesteyn HME, Kotecha A, Ginn HM, Hecksel CW, Beale EV, de Haas F, Evans G, Zhang P, Chiu W, Stuart DI. Machining protein microcrystals for structure determination by electron diffraction. Proc Natl Acad Sci U S A 2018; 115:9569-9573. [PMID: 30171169 PMCID: PMC6156647 DOI: 10.1073/pnas.1809978115] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We demonstrate that ion-beam milling of frozen, hydrated protein crystals to thin lamella preserves the crystal lattice to near-atomic resolution. This provides a vehicle for protein structure determination, bridging the crystal size gap between the nanometer scale of conventional electron diffraction and micron scale of synchrotron microfocus beamlines. The demonstration that atomic information can be retained suggests that milling could provide such detail on sections cut from vitrified cells.
Collapse
Affiliation(s)
- Helen M E Duyvesteyn
- Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Abhay Kotecha
- Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, United Kingdom
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, The Netherlands
| | - Helen M Ginn
- Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Corey W Hecksel
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Emma V Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Felix de Haas
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, The Netherlands
| | - Gwyndaf Evans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Peijun Zhang
- Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305;
- CryoEM and Bioimaging Division, SSRL SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - David I Stuart
- Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, United Kingdom;
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| |
Collapse
|
25
|
Abstract
G protein-coupled receptors (GPCRs) represent a large superfamily of membrane proteins that mediate cell signaling and regulate a variety of physiological processes in the human body. Structure-function studies of this superfamily were enabled a decade ago by multiple breakthroughs in technology that included receptor stabilization, crystallization in a membrane environment, and microcrystallography. The recent emergence of X-ray free-electron lasers (XFELs) has further accelerated structural studies of GPCRs and other challenging proteins by overcoming radiation damage and providing access to high-resolution structures and dynamics using micrometer-sized crystals. Here, we summarize key technology advancements and major milestones of GPCR research using XFELs and provide a brief outlook on future developments in the field.
Collapse
Affiliation(s)
- Benjamin Stauch
- Department of Chemistry and Bridge Institute, University of Southern California, Los Angeles, California 90089, USA; ,
| | - Vadim Cherezov
- Department of Chemistry and Bridge Institute, University of Southern California, Los Angeles, California 90089, USA; ,
| |
Collapse
|
26
|
Mizohata E, Nakane T, Fukuda Y, Nango E, Iwata S. Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology. Biophys Rev 2017; 10:209-218. [PMID: 29196935 DOI: 10.1007/s12551-017-0344-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/13/2017] [Indexed: 12/16/2022] Open
Abstract
X-ray crystallography visualizes the world at the atomic level. It has been used as the most powerful technique for observing the three-dimensional structures of biological macromolecules and has pioneered structural biology. To determine a crystal structure with high resolution, it was traditionally required to prepare large crystals (> 200 μm). Later, synchrotron radiation facilities, such as SPring-8, that produce powerful X-rays were built. They enabled users to obtain good quality X-ray diffraction images even with smaller crystals (ca. 200-50 μm). In recent years, one of the most important technological innovations in structural biology has been the development of X-ray free electron lasers (XFELs). The SPring-8 Angstrom Compact free electron LAser (SACLA) in Japan generates the XFEL beam by accelerating electrons to relativistic speeds and directing them through in-vacuum, short-period undulators. Since user operation started in 2012, we have been involved in the development of serial femtosecond crystallography (SFX) measurement systems using XFEL at the SACLA. The SACLA generates X-rays a billion times brighter than SPring-8. The extremely bright XFEL pulses enable data collection with microcrystals (ca. 50-1 μm). Although many molecular analysis techniques exist, SFX is the only technique that can visualize radiation-damage-free structures of biological macromolecules at room temperature in atomic resolution and fast time resolution. Here, we review the achievements of the SACLA-SFX Project in the past 5 years. In particular, we focus on: (1) the measurement system for SFX; (2) experimental phasing by SFX; (3) enzyme chemistry based on damage-free room-temperature structures; and (4) molecular movie taken by time-resolved SFX.
Collapse
Affiliation(s)
- Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 OQH, UK
| | - Yohta Fukuda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.,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, Hyogo, 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| |
Collapse
|
27
|
X-ray free electron laser: opportunities for drug discovery. Essays Biochem 2017; 61:529-542. [PMID: 29118098 DOI: 10.1042/ebc20170031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 01/16/2023]
Abstract
Past decades have shown the impact of structural information derived from complexes of drug candidates with their protein targets to facilitate the discovery of safe and effective medicines. Despite recent developments in single particle cryo-electron microscopy, X-ray crystallography has been the main method to derive structural information. The unique properties of X-ray free electron laser (XFEL) with unmet peak brilliance and beam focus allow X-ray diffraction data recording and successful structure determination from smaller and weaker diffracting crystals shortening timelines in crystal optimization. To further capitalize on the XFEL advantage, innovations in crystal sample delivery for the X-ray experiment, data collection and processing methods are required. This development was a key contributor to serial crystallography allowing structure determination at room temperature yielding physiologically more relevant structures. Adding the time resolution provided by the femtosecond X-ray pulse will enable monitoring and capturing of dynamic processes of ligand binding and associated conformational changes with great impact to the design of candidate drug compounds.
Collapse
|
28
|
Ginn HM, Stuart DI. The slip-and-slide algorithm: a refinement protocol for detector geometry. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:1152-1162. [PMID: 29091058 PMCID: PMC5665294 DOI: 10.1107/s1600577517013327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/18/2017] [Indexed: 06/07/2023]
Abstract
Geometry correction is traditionally plagued by mis-fitting of correlated parameters, leading to local minima which prevent further improvements. Segmented detectors pose an enhanced risk of mis-fitting: even a minor confusion of detector distance and panel separation can prevent improvement in data quality. The slip-and-slide algorithm breaks down effects of the correlated parameters and their associated target functions in a fundamental shift in the approach to the problem. Parameters are never refined against the components of the data to which they are insensitive, providing a dramatic boost in the exploitation of information from a very small number of diffraction patterns. This algorithm can be applied to exploit the adherence of the spot-finding results prior to indexing to a given lattice using unit-cell dimensions as a restraint. Alternatively, it can be applied to the predicted spot locations and the observed reflection positions after indexing from a smaller number of images. Thus, the indexing rate can be boosted by 5.8% using geometry refinement from only 125 indexed patterns or 500 unindexed patterns. In one example of cypovirus type 17 polyhedrin diffraction at the Linac Coherent Light Source, this geometry refinement reveals a detector tilt of 0.3° (resulting in a maximal Z-axis error of ∼0.5 mm from an average detector distance of ∼90 mm) whilst treating all panels independently. Re-indexing and integrating with updated detector geometry reduces systematic errors providing a boost in anomalous signal of sulfur atoms by 20%. Due to the refinement of decoupled parameters, this geometry method also reaches convergence.
Collapse
Affiliation(s)
- Helen Mary Ginn
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
- Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, UK
| | - David Ian Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
- Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, UK
| |
Collapse
|
29
|
Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons. Nat Commun 2017; 8:542. [PMID: 28912485 PMCID: PMC5599499 DOI: 10.1038/s41467-017-00630-4] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/14/2017] [Indexed: 12/24/2022] Open
Abstract
Historically, room-temperature structure determination was succeeded by cryo-crystallography to mitigate radiation damage. Here, we demonstrate that serial millisecond crystallography at a synchrotron beamline equipped with high-viscosity injector and high frame-rate detector allows typical crystallographic experiments to be performed at room-temperature. Using a crystal scanning approach, we determine the high-resolution structure of the radiation sensitive molybdenum storage protein, demonstrate soaking of the drug colchicine into tubulin and native sulfur phasing of the human G protein-coupled adenosine receptor. Serial crystallographic data for molecular replacement already converges in 1,000–10,000 diffraction patterns, which we collected in 3 to maximally 82 minutes. Compared with serial data we collected at a free-electron laser, the synchrotron data are of slightly lower resolution, however fewer diffraction patterns are needed for de novo phasing. Overall, the data we collected by room-temperature serial crystallography are of comparable quality to cryo-crystallographic data and can be routinely collected at synchrotrons. Serial crystallography was developed for protein crystal data collection with X-ray free-electron lasers. Here the authors present several examples which show that serial crystallography using high-viscosity injectors can also be routinely employed for room-temperature data collection at synchrotrons.
Collapse
|
30
|
Hutchison CDM, Cordon-Preciado V, Morgan RML, Nakane T, Ferreira J, Dorlhiac G, Sanchez-Gonzalez A, Johnson AS, Fitzpatrick A, Fare C, Marangos JP, Yoon CH, Hunter MS, DePonte DP, Boutet S, Owada S, Tanaka R, Tono K, Iwata S, van Thor JJ. X-ray Free Electron Laser Determination of Crystal Structures of Dark and Light States of a Reversibly Photoswitching Fluorescent Protein at Room Temperature. Int J Mol Sci 2017; 18:E1918. [PMID: 28880248 PMCID: PMC5618567 DOI: 10.3390/ijms18091918] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/01/2017] [Accepted: 09/02/2017] [Indexed: 01/03/2023] Open
Abstract
The photochromic fluorescent protein Skylan-NS (Nonlinear Structured illumination variant mEos3.1H62L) is a reversibly photoswitchable fluorescent protein which has an unilluminated/ground state with an anionic and cis chromophore conformation and high fluorescence quantum yield. Photo-conversion with illumination at 515 nm generates a meta-stable intermediate with neutral trans-chromophore structure that has a 4 h lifetime. We present X-ray crystal structures of the cis (on) state at 1.9 Angstrom resolution and the trans (off) state at a limiting resolution of 1.55 Angstrom from serial femtosecond crystallography experiments conducted at SPring-8 Angstrom Compact Free Electron Laser (SACLA) at 7.0 keV and 10.5 keV, and at Linac Coherent Light Source (LCLS) at 9.5 keV. We present a comparison of the data reduction and structure determination statistics for the two facilities which differ in flux, beam characteristics and detector technologies. Furthermore, a comparison of droplet on demand, grease injection and Gas Dynamic Virtual Nozzle (GDVN) injection shows no significant differences in limiting resolution. The photoconversion of the on- to the off-state includes both internal and surface exposed protein structural changes, occurring in regions that lack crystal contacts in the orthorhombic crystal form.
Collapse
Affiliation(s)
- Christopher D. M. Hutchison
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Violeta Cordon-Preciado
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Rhodri M. L. Morgan
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan;
| | - Josie Ferreira
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Gabriel Dorlhiac
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Alvaro Sanchez-Gonzalez
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College, London SW7 2AZ, UK; (A.S.-G.); (A.S.J.); (J.P.M.)
| | - Allan S. Johnson
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College, London SW7 2AZ, UK; (A.S.-G.); (A.S.J.); (J.P.M.)
| | - Ann Fitzpatrick
- Diamond Light Source Ltd., Diamond House, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK;
| | - Clyde Fare
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| | - Jon P. Marangos
- Quantum Optics and Laser Science Group, Blackett Laboratory, Imperial College, London SW7 2AZ, UK; (A.S.-G.); (A.S.J.); (J.P.M.)
| | - Chun Hong Yoon
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA; (C.H.Y.); (M.S.H.); (D.P.D.); (S.B.)
| | - Mark S. Hunter
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA; (C.H.Y.); (M.S.H.); (D.P.D.); (S.B.)
| | - Daniel P. DePonte
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA; (C.H.Y.); (M.S.H.); (D.P.D.); (S.B.)
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA; (C.H.Y.); (M.S.H.); (D.P.D.); (S.B.)
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5148, Japan; (S.O.); (R.T.); (K.T.); (S.I.)
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5148, Japan; (S.O.); (R.T.); (K.T.); (S.I.)
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5148, Japan; (S.O.); (R.T.); (K.T.); (S.I.)
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5198, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Hyogo 679-5148, Japan; (S.O.); (R.T.); (K.T.); (S.I.)
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Jasper J. van Thor
- Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK; (C.D.M.H.); (V.C.-P.); (J.F.); (G.D.); (C.F.)
| |
Collapse
|
31
|
Yamashita K, Kuwabara N, Nakane T, Murai T, Mizohata E, Sugahara M, Pan D, Masuda T, Suzuki M, Sato T, Kodan A, Yamaguchi T, Nango E, Tanaka T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Manya H, Endo T, Kato R, Senda T, Kato H, Iwata S, Ago H, Yamamoto M, Yumoto F, Nakatsu T. Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography. IUCRJ 2017; 4:639-647. [PMID: 28989719 PMCID: PMC5619855 DOI: 10.1107/s2052252517008557] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/08/2017] [Indexed: 05/31/2023]
Abstract
Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) holds enormous potential for the structure determination of proteins for which it is difficult to produce large and high-quality crystals. SFX has been applied to various systems, but rarely to proteins that have previously unknown structures. Consequently, the majority of previously obtained SFX structures have been solved by the molecular replacement method. To facilitate protein structure determination by SFX, it is essential to establish phasing methods that work efficiently for SFX. Here, selenomethionine derivatization and mercury soaking have been investigated for SFX experiments using the high-energy XFEL at the SPring-8 Angstrom Compact Free-Electron Laser (SACLA), Hyogo, Japan. Three successful cases are reported of single-wavelength anomalous diffraction (SAD) phasing using X-rays of less than 1 Å wavelength with reasonable numbers of diffraction patterns (13 000, 60 000 and 11 000). It is demonstrated that the combination of high-energy X-rays from an XFEL and commonly used heavy-atom incorporation techniques will enable routine de novo structural determination of biomacromolecules.
Collapse
Affiliation(s)
- Keitaro Yamashita
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Naoyuki Kuwabara
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomohiro Murai
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Dongqing Pan
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tetsuya Masuda
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Mamoru Suzuki
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomomi Sato
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Atsushi Kodan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomohiro Yamaguchi
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takashi Kameshima
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takaki Hatsui
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hiroshi Manya
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Tamao Endo
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Ryuichi Kato
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Hiroaki Kato
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hideo Ago
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Fumiaki Yumoto
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toru Nakatsu
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| |
Collapse
|
32
|
Johansson LC, Stauch B, Ishchenko A, Cherezov V. A Bright Future for Serial Femtosecond Crystallography with XFELs. Trends Biochem Sci 2017; 42:749-762. [PMID: 28733116 DOI: 10.1016/j.tibs.2017.06.007] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 11/19/2022]
Abstract
X-ray free electron lasers (XFELs) have the potential to revolutionize macromolecular structural biology due to the unique combination of spatial coherence, extreme peak brilliance, and short duration of X-ray pulses. A recently emerged serial femtosecond (fs) crystallography (SFX) approach using XFEL radiation overcomes some of the biggest hurdles of traditional crystallography related to radiation damage through the diffraction-before-destruction principle. Intense fs XFEL pulses enable high-resolution room-temperature structure determination of difficult-to-crystallize biological macromolecules, while simultaneously opening a new era of time-resolved structural studies. Here, we review the latest developments in instrumentation, sample delivery, data analysis, crystallization methods, and applications of SFX to important biological questions, and conclude with brief insights into the bright future of structural biology using XFELs.
Collapse
Affiliation(s)
- Linda C Johansson
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Benjamin Stauch
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA.
| |
Collapse
|
33
|
Spence JCH. XFELs for structure and dynamics in biology. IUCRJ 2017; 4:322-339. [PMID: 28875020 PMCID: PMC5571796 DOI: 10.1107/s2052252517005760] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/17/2017] [Indexed: 05/20/2023]
Abstract
The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are outlined, and some grand challenges are suggested. By avoiding the need to cool samples to minimize damage, the XFEL has permitted atomic resolution imaging of molecular processes on the 100 fs timescale under near-physiological conditions and in the correct thermal bath in which molecular machines operate. Radiation damage, comparisons of XFEL and synchrotron work, single-particle diffraction, fast solution scattering, pump-probe studies on photosensitive proteins, mix-and-inject experiments, caged molecules, pH jump and other reaction-initiation methods, and the study of molecular machines are all discussed. Sample-delivery methods and data-analysis algorithms for the various modes, from serial femtosecond crystallo-graphy to fast solution scattering, fluctuation X-ray scattering, mixing jet experiments and single-particle diffraction, are also reviewed.
Collapse
Affiliation(s)
- J. C. H. Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| |
Collapse
|
34
|
Masuda T, Suzuki M, Inoue S, Song C, Nakane T, Nango E, Tanaka R, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Mikami B, Nureki O, Numata K, Iwata S, Sugahara M. Atomic resolution structure of serine protease proteinase K at ambient temperature. Sci Rep 2017; 7:45604. [PMID: 28361898 PMCID: PMC5374539 DOI: 10.1038/srep45604] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/01/2017] [Indexed: 01/24/2023] Open
Abstract
Atomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites.
Collapse
Affiliation(s)
- Tetsuya Masuda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.,RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mamoru Suzuki
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigeyuki Inoue
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Changyong Song
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Physics, POSTECH, Pohang 790-784, Korea
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takashi Kameshima
- Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takaki Hatsui
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Bunzo Mikami
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keiji Numata
- Enzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - So Iwata
- RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | | |
Collapse
|
35
|
|
36
|
Abstract
AbstractIn 1912, Max von Laue and collaborators first observed diffraction spots from a millimeter-sized crystal of copper sulfate using an X-ray tube. Crystallography was born of this experiment, and since then, diffraction by both X-rays and electrons has revealed a myriad of inorganic and organic structures, including structures of complex protein assemblies. Advancements in X-ray sources have spurred a revolution in structure determination, facilitated by the development of new methods. This review explores some of the frontier methods that are shaping the future of X-ray diffraction, including coherent diffractive imaging, serial femtosecond X-ray crystallography and small-angle X-ray scattering. Collectively, these methods expand the current limits of structure determination in biological systems across multiple length and time scales.
Collapse
|
37
|
Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent. Proc Natl Acad Sci U S A 2016; 113:13039-13044. [PMID: 27799539 DOI: 10.1073/pnas.1602531113] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 3D structure determination of biological macromolecules by X-ray crystallography suffers from a phase problem: to perform Fourier transformation to calculate real space density maps, both intensities and phases of structure factors are necessary; however, measured diffraction patterns give only intensities. Although serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has been steadily developed since 2009, experimental phasing still remains challenging. Here, using 7.0-keV (1.771 Å) X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (SACLA), iodine single-wavelength anomalous diffraction (SAD), single isomorphous replacement (SIR), and single isomorphous replacement with anomalous scattering (SIRAS) phasing were performed in an SFX regime for a model membrane protein bacteriorhodopsin (bR). The crystals grown in bicelles were derivatized with an iodine-labeled detergent heavy-atom additive 13a (HAD13a), which contains the magic triangle, I3C head group with three iodine atoms. The alkyl tail was essential for binding of the detergent to the surface of bR. Strong anomalous and isomorphous difference signals from HAD13a enabled successful phasing using reflections up to 2.1-Å resolution from only 3,000 and 4,000 indexed images from native and derivative crystals, respectively. When more images were merged, structure solution was possible with data truncated at 3.3-Å resolution, which is the lowest resolution among the reported cases of SFX phasing. Moreover, preliminary SFX experiment showed that HAD13a successfully derivatized the G protein-coupled A2a adenosine receptor crystallized in lipidic cubic phases. These results pave the way for de novo structure determination of membrane proteins, which often diffract poorly, even with the brightest XFEL beams.
Collapse
|
38
|
Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Zhou Q, Zhao M, Brewster AS, Michels-Clark T, Holton JM, Sauter NK, Weis WI, Brunger AT. Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex. eLife 2016; 5. [PMID: 27731796 PMCID: PMC5094853 DOI: 10.7554/elife.18740] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 10/11/2016] [Indexed: 12/03/2022] Open
Abstract
X-ray free electron lasers (XFELs) reduce the effects of radiation damage on macromolecular diffraction data and thereby extend the limiting resolution. Previously, we adapted classical post-refinement techniques to XFEL diffraction data to produce accurate diffraction data sets from a limited number of diffraction images (Uervirojnangkoorn et al., 2015), and went on to use these techniques to obtain a complete data set from crystals of the synaptotagmin-1 / SNARE complex and to determine the structure at 3.5 Å resolution (Zhou et al., 2015). Here, we describe new advances in our methods and present a reprocessed XFEL data set of the synaptotagmin-1 / SNARE complex. The reprocessing produced small improvements in electron density maps and the refined atomic model. The maps also contained more information than those of a lower resolution (4.1 Å) synchrotron data set. Processing a set of simulated XFEL diffraction images revealed that our methods yield accurate data and atomic models. DOI:http://dx.doi.org/10.7554/eLife.18740.001
Collapse
Affiliation(s)
- Artem Y Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Oliver B Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Minglei Zhao
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| |
Collapse
|
39
|
|
40
|
Oghbaey S, Sarracini A, Ginn HM, Pare-Labrosse O, Kuo A, Marx A, Epp SW, Sherrell DA, Eger BT, Zhong Y, Loch R, Mariani V, Alonso-Mori R, Nelson S, Lemke HT, Owen RL, Pearson AR, Stuart DI, Ernst OP, Mueller-Werkmeister HM, Miller RJD. Fixed target combined with spectral mapping: approaching 100% hit rates for serial crystallography. Acta Crystallogr D Struct Biol 2016; 72:944-55. [PMID: 27487825 PMCID: PMC5937680 DOI: 10.1107/s2059798316010834] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 07/04/2016] [Indexed: 11/10/2022] Open
Abstract
The advent of ultrafast highly brilliant coherent X-ray free-electron laser sources has driven the development of novel structure-determination approaches for proteins, and promises visualization of protein dynamics on sub-picosecond timescales with full atomic resolution. Significant efforts are being applied to the development of sample-delivery systems that allow these unique sources to be most efficiently exploited for high-throughput serial femtosecond crystallography. Here, the next iteration of a fixed-target crystallography chip designed for rapid and reliable delivery of up to 11 259 protein crystals with high spatial precision is presented. An experimental scheme for predetermining the positions of crystals in the chip by means of in situ spectroscopy using a fiducial system for rapid, precise alignment and registration of the crystal positions is presented. This delivers unprecedented performance in serial crystallography experiments at room temperature under atmospheric pressure, giving a raw hit rate approaching 100% with an effective indexing rate of approximately 50%, increasing the efficiency of beam usage and allowing the method to be applied to systems where the number of crystals is limited.
Collapse
Affiliation(s)
- Saeed Oghbaey
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
| | - Antoine Sarracini
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
| | - Helen M. Ginn
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire, OX3 7BN, UK
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Olivier Pare-Labrosse
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
| | - Anling Kuo
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
| | - Alexander Marx
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Sascha W. Epp
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Darren A. Sherrell
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Bryan T. Eger
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
| | - Yinpeng Zhong
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Rolf Loch
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Desy, 22607, Hamburg, Germany
| | - Roberto Alonso-Mori
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Silke Nelson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Henrik T. Lemke
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Robin L. Owen
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Arwen R. Pearson
- Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany
| | - David I. Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire, OX3 7BN, UK
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Oliver P. Ernst
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Henrike M. Mueller-Werkmeister
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - R. J. Dwayne Miller
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany
| |
Collapse
|
41
|
Ginn HM, Roedig P, Kuo A, Evans G, Sauter NK, Ernst OP, Meents A, Mueller-Werkmeister H, Miller RJD, Stuart DI. TakeTwo: an indexing algorithm suited to still images with known crystal parameters. Acta Crystallogr D Struct Biol 2016; 72:956-65. [PMID: 27487826 PMCID: PMC4973211 DOI: 10.1107/s2059798316010706] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/01/2016] [Indexed: 11/10/2022] Open
Abstract
The indexing methods currently used for serial femtosecond crystallography were originally developed for experiments in which crystals are rotated in the X-ray beam, providing significant three-dimensional information. On the other hand, shots from both X-ray free-electron lasers and serial synchrotron crystallography experiments are still images, in which the few three-dimensional data available arise only from the curvature of the Ewald sphere. Traditional synchrotron crystallography methods are thus less well suited to still image data processing. Here, a new indexing method is presented with the aim of maximizing information use from a still image given the known unit-cell dimensions and space group. Efficacy for cubic, hexagonal and orthorhombic space groups is shown, and for those showing some evidence of diffraction the indexing rate ranged from 90% (hexagonal space group) to 151% (cubic space group). Here, the indexing rate refers to the number of lattices indexed per image.
Collapse
Affiliation(s)
- Helen Mary Ginn
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
| | - Philip Roedig
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anling Kuo
- Department of Biochemistry, University of Toronto, King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Gwyndaf Evans
- Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, England
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Alke Meents
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - R J Dwayne Miller
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - David Ian Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
| |
Collapse
|
42
|
Ginn HM, Evans G, Sauter NK, Stuart DI. On the release of cppxfel for processing X-ray free-electron laser images. J Appl Crystallogr 2016; 49:1065-1072. [PMID: 27275149 PMCID: PMC4886992 DOI: 10.1107/s1600576716006981] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/25/2016] [Indexed: 12/21/2022] Open
Abstract
As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here cppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set. Cppxfel is released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.
Collapse
Affiliation(s)
- Helen Mary Ginn
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - Gwyndaf Evans
- Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, Didcot, Oxfordshire OX11 QX, UK
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - David Ian Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
- Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, Didcot, Oxfordshire OX11 QX, UK
| |
Collapse
|
43
|
Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Brewster AS, Murray TD, Sauter NK, Berger JM, Weis WI, Brunger AT. IOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction images. J Appl Crystallogr 2016; 49:1057-1064. [PMID: 27275148 PMCID: PMC4886991 DOI: 10.1107/s1600576716006683] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/19/2016] [Indexed: 01/25/2023] Open
Abstract
Serial femtosecond crystallography (SFX) uses an X-ray free-electron laser to extract diffraction data from crystals not amenable to conventional X-ray light sources owing to their small size or radiation sensitivity. However, a limitation of SFX is the high variability of the diffraction images that are obtained. As a result, it is often difficult to determine optimal indexing and integration parameters for the individual diffraction images. Presented here is a software package, called IOTA, which uses a grid-search technique to determine optimal spot-finding parameters that can in turn affect the success of indexing and the quality of integration on an image-by-image basis. Integration results can be filtered using a priori information about the Bravais lattice and unit-cell dimensions and analyzed for unit-cell isomorphism, facilitating an improvement in subsequent data-processing steps.
Collapse
Affiliation(s)
- Artem Y. Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Oliver B. Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas D. Murray
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William I. Weis
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
44
|
Nakane T, Joti Y, Tono K, Yabashi M, Nango E, Iwata S, Ishitani R, Nureki O. Data processing pipeline for serial femtosecond crystallography at SACLA. J Appl Crystallogr 2016; 49:1035-1041. [PMID: 27275146 PMCID: PMC4886989 DOI: 10.1107/s1600576716005720] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/06/2016] [Indexed: 11/10/2022] Open
Abstract
A data processing pipeline for serial femtosecond crystallography at SACLA was developed, based on Cheetah [Barty et al. (2014). J. Appl. Cryst.47, 1118-1131] and CrystFEL [White et al. (2016). J. Appl. Cryst.49, 680-689]. The original programs were adapted for data acquisition through the SACLA API, thread and inter-node parallelization, and efficient image handling. The pipeline consists of two stages: The first, online stage can analyse all images in real time, with a latency of less than a few seconds, to provide feedback on hit rate and detector saturation. The second, offline stage converts hit images into HDF5 files and runs CrystFEL for indexing and integration. The size of the filtered compressed output is comparable to that of a synchrotron data set. The pipeline enables real-time feedback and rapid structure solution during beamtime.
Collapse
Affiliation(s)
- Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Makina Yabashi
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| |
Collapse
|
45
|
Nass K, Meinhart A, Barends TRM, Foucar L, Gorel A, Aquila A, Botha S, Doak RB, Koglin J, Liang M, Shoeman RL, Williams G, Boutet S, Schlichting I. Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data. IUCRJ 2016; 3:180-91. [PMID: 27158504 PMCID: PMC4856140 DOI: 10.1107/s2052252516002980] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/18/2016] [Indexed: 05/23/2023]
Abstract
Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems that are prone to radiation damage. However, phasing XFEL data de novo is complicated by the inherent inaccuracy of SFX data, and only a few successful examples, mostly based on exceedingly strong anomalous or isomorphous difference signals, have been reported. Here, it is shown that SFX data from thaumatin microcrystals can be successfully phased using only the weak anomalous scattering from the endogenous S atoms. Moreover, a step-by-step investigation is presented of the particular problems of SAD phasing of SFX data, analysing data from a derivative with a strong anomalous signal as well as the weak signal from endogenous S atoms.
Collapse
Affiliation(s)
- Karol Nass
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Anton Meinhart
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Lutz Foucar
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Alexander Gorel
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Andrew Aquila
- European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Sabine Botha
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - R. Bruce Doak
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jason Koglin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mengning Liang
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Robert L. Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Garth Williams
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sebastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| |
Collapse
|
46
|
White TA, Mariani V, Brehm W, Yefanov O, Barty A, Beyerlein KR, Chervinskii F, Galli L, Gati C, Nakane T, Tolstikova A, Yamashita K, Yoon CH, Diederichs K, Chapman HN. Recent developments in CrystFEL. J Appl Crystallogr 2016; 49:680-689. [PMID: 27047311 PMCID: PMC4815879 DOI: 10.1107/s1600576716004751] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/21/2016] [Indexed: 12/04/2022] Open
Abstract
CrystFEL is a suite of programs for processing data from 'serial crystallography' experiments, which are usually performed using X-ray free-electron lasers (FELs) but also increasingly with other X-ray sources. The CrystFEL software suite has been under development since 2009, just before the first hard FEL experiments were performed, and has been significantly updated and improved since then. This article describes the most important improvements which have been made to CrystFEL since the first release version. These changes include the addition of new programs to the suite, the ability to resolve 'indexing ambiguities' and several ways to improve the quality of the integrated data by more accurately modelling the underlying diffraction physics.
Collapse
Affiliation(s)
- Thomas A. White
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Valerio Mariani
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Department of Biology, Universität Konstanz, Box 647, 78457 Konstanz, Germany
| | - Oleksandr Yefanov
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kenneth R. Beyerlein
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Fedor Chervinskii
- Moscow Institute of Physics and Technology, 141700 Moscow, Russian Federation
| | - Lorenzo Galli
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Cornelius Gati
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Alexandra Tolstikova
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Chun Hong Yoon
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kay Diederichs
- Department of Biology, Universität Konstanz, Box 647, 78457 Konstanz, Germany
| | - Henry N. Chapman
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| |
Collapse
|
47
|
Jaeger K, Dworkowski F, Nogly P, Milne C, Wang M, Standfuss J. Serial Millisecond Crystallography of Membrane Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:137-149. [DOI: 10.1007/978-3-319-35072-1_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
|
48
|
Ji X, Axford D, Owen R, Evans G, Ginn HM, Sutton G, Stuart DI. Polyhedra structures and the evolution of the insect viruses. J Struct Biol 2015; 192:88-99. [PMID: 26291392 PMCID: PMC4597613 DOI: 10.1016/j.jsb.2015.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 08/07/2015] [Accepted: 08/17/2015] [Indexed: 01/07/2023]
Abstract
Polyhedra represent an ancient system used by a number of insect viruses to protect virions during long periods of environmental exposure. We present high resolution crystal structures of polyhedra for seven previously uncharacterised types of cypoviruses, four using ab initio selenomethionine phasing (two of these required over 100 selenomethionine crystals each). Approximately 80% of residues are structurally equivalent between all polyhedrins (pairwise rmsd ⩽ 1.5 Å), whilst pairwise sequence identities, based on structural alignment, are as little as 12%. These structures illustrate the effect of 400 million years of evolution on a system where the crystal lattice is the functionally conserved feature in the face of massive sequence variability. The conservation of crystal contacts is maintained across most of the molecular surface, except for a dispensable virus recognition domain. By spreading the contacts over so much of the protein surface the lattice remains robust in the face of many individual changes. Overall these unusual structural constraints seem to have skewed the molecule's evolution so that surface residues are almost as conserved as the internal residues.
Collapse
Affiliation(s)
- Xiaoyun Ji
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom
| | - Danny Axford
- Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Robin Owen
- Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Gwyndaf Evans
- Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Helen M. Ginn
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom
| | - Geoff Sutton
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom
| | - David I. Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom,Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom,Corresponding author at: Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom.Division of Structural BiologyThe Wellcome Trust Centre for Human GeneticsUniversity of OxfordRoosevelt DriveOxfordOxfordshireOX3 7BNUnited Kingdom
| |
Collapse
|