Single-particle imaging without symmetry constraints at an X-ray free-electron laser
The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of sever...
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doaj-670e83fa3c454ffab30f60db6849408c2020-11-24T21:35:03ZengInternational Union of CrystallographyIUCrJ2052-25252018-11-015672773610.1107/S205225251801120Xit5017Single-particle imaging without symmetry constraints at an X-ray free-electron laserMax Rose0Sergey Bobkov1Kartik Ayyer2Ruslan P. Kurta3Dmitry Dzhigaev4Young Yong Kim5Andrew J. Morgan6Chun Hong Yoon7Daniel Westphal8Johan Bielecki9Jonas A. Sellberg10Garth Williams11Filipe R.N.C. Maia12Olexander M. Yefanov13Vyacheslav Ilyin14Adrian P. Mancuso15Henry N. Chapman16Brenda G. Hogue17Andrew Aquila18Anton Barty19Ivan A. Vartanyants20Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg D-22607, GermanyNational Research Centre 'Kurchatov Institute', Akademika Kurchatova pl. 1, Moscow 123182, RussiaCenter for Free Electron Laser Science (CFEL), Notkestrasse 85, Hamburg 22607, GermanyEuropean XFEL GmbH, Holzkoppel 4, Schenefeld 22869, GermanyDeutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg D-22607, GermanyDeutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg D-22607, GermanyCenter for Free Electron Laser Science (CFEL), Notkestrasse 85, Hamburg 22607, GermanyLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USALaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SwedenEuropean XFEL GmbH, Holzkoppel 4, Schenefeld 22869, GermanyLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SwedenBrookhaven National Laboratory, 98 Rochester St, Shirley, NY 11967, USALaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SwedenCenter for Free Electron Laser Science (CFEL), Notkestrasse 85, Hamburg 22607, GermanyNational Research Centre 'Kurchatov Institute', Akademika Kurchatova pl. 1, Moscow 123182, RussiaEuropean XFEL GmbH, Holzkoppel 4, Schenefeld 22869, GermanyCenter for Free Electron Laser Science (CFEL), Notkestrasse 85, Hamburg 22607, GermanyBiodesign Center for Immunotherapy, Vaccines, and Virotherapy, Biodesign Institute at Arizona State University, Tempe 85287, USALinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USACenter for Free Electron Laser Science (CFEL), Notkestrasse 85, Hamburg 22607, GermanyDeutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg D-22607, GermanyThe analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of several well defined steps including single-hit diffraction data classification, refined filtering of the classified data, reconstruction of three-dimensional scattered intensity from the experimental diffraction patterns by orientation determination and a final three-dimensional reconstruction of the virus electron density without symmetry constraints. The analysis developed here revealed and quantified nanoscale features of the PR772 virus measured in this experiment, with the obtained resolution better than 10 nm, with a clear indication that the structure was compressed in one direction and, as such, deviates from ideal icosahedral symmetry.http://scripts.iucr.org/cgi-bin/paper?S205225251801120Xsingle-particle imagingthree-dimensional virus reconstructionsXFELs |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Max Rose Sergey Bobkov Kartik Ayyer Ruslan P. Kurta Dmitry Dzhigaev Young Yong Kim Andrew J. Morgan Chun Hong Yoon Daniel Westphal Johan Bielecki Jonas A. Sellberg Garth Williams Filipe R.N.C. Maia Olexander M. Yefanov Vyacheslav Ilyin Adrian P. Mancuso Henry N. Chapman Brenda G. Hogue Andrew Aquila Anton Barty Ivan A. Vartanyants |
spellingShingle |
Max Rose Sergey Bobkov Kartik Ayyer Ruslan P. Kurta Dmitry Dzhigaev Young Yong Kim Andrew J. Morgan Chun Hong Yoon Daniel Westphal Johan Bielecki Jonas A. Sellberg Garth Williams Filipe R.N.C. Maia Olexander M. Yefanov Vyacheslav Ilyin Adrian P. Mancuso Henry N. Chapman Brenda G. Hogue Andrew Aquila Anton Barty Ivan A. Vartanyants Single-particle imaging without symmetry constraints at an X-ray free-electron laser IUCrJ single-particle imaging three-dimensional virus reconstructions XFELs |
author_facet |
Max Rose Sergey Bobkov Kartik Ayyer Ruslan P. Kurta Dmitry Dzhigaev Young Yong Kim Andrew J. Morgan Chun Hong Yoon Daniel Westphal Johan Bielecki Jonas A. Sellberg Garth Williams Filipe R.N.C. Maia Olexander M. Yefanov Vyacheslav Ilyin Adrian P. Mancuso Henry N. Chapman Brenda G. Hogue Andrew Aquila Anton Barty Ivan A. Vartanyants |
author_sort |
Max Rose |
title |
Single-particle imaging without symmetry constraints at an X-ray free-electron laser |
title_short |
Single-particle imaging without symmetry constraints at an X-ray free-electron laser |
title_full |
Single-particle imaging without symmetry constraints at an X-ray free-electron laser |
title_fullStr |
Single-particle imaging without symmetry constraints at an X-ray free-electron laser |
title_full_unstemmed |
Single-particle imaging without symmetry constraints at an X-ray free-electron laser |
title_sort |
single-particle imaging without symmetry constraints at an x-ray free-electron laser |
publisher |
International Union of Crystallography |
series |
IUCrJ |
issn |
2052-2525 |
publishDate |
2018-11-01 |
description |
The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of several well defined steps including single-hit diffraction data classification, refined filtering of the classified data, reconstruction of three-dimensional scattered intensity from the experimental diffraction patterns by orientation determination and a final three-dimensional reconstruction of the virus electron density without symmetry constraints. The analysis developed here revealed and quantified nanoscale features of the PR772 virus measured in this experiment, with the obtained resolution better than 10 nm, with a clear indication that the structure was compressed in one direction and, as such, deviates from ideal icosahedral symmetry. |
topic |
single-particle imaging three-dimensional virus reconstructions XFELs |
url |
http://scripts.iucr.org/cgi-bin/paper?S205225251801120X |
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