IUCrJ (Nov 2020)
An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser
- Dameli Assalauova,
- Young Yong Kim,
- Sergey Bobkov,
- Ruslan Khubbutdinov,
- Max Rose,
- Roberto Alvarez,
- Jakob Andreasson,
- Eugeniu Balaur,
- Alice Contreras,
- Hasan DeMirci,
- Luca Gelisio,
- Janos Hajdu,
- Mark S. Hunter,
- Ruslan P. Kurta,
- Haoyuan Li,
- Matthew McFadden,
- Reza Nazari,
- Peter Schwander,
- Anton Teslyuk,
- Peter Walter,
- P. Lourdu Xavier,
- Chun Hong Yoon,
- Sahba Zaare,
- Viacheslav A. Ilyin,
- Richard A. Kirian,
- Brenda G. Hogue,
- Andrew Aquila,
- Ivan A. Vartanyants
Affiliations
- Dameli Assalauova
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- Young Yong Kim
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- Sergey Bobkov
- National Research Center `Kurchatov Institute', Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
- Ruslan Khubbutdinov
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- Max Rose
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- Roberto Alvarez
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- Jakob Andreasson
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic
- Eugeniu Balaur
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria 3086, Australia
- Alice Contreras
- School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
- Hasan DeMirci
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Luca Gelisio
- Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany
- Janos Hajdu
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic
- Mark S. Hunter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Ruslan P. Kurta
- European XFEL, Holzkoppel 4, Schenefeld, D-22869, Germany
- Haoyuan Li
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Matthew McFadden
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
- Reza Nazari
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- Peter Schwander
- University of Wisconsin Milwaukee, Milwaukee WI 53211, USA
- Anton Teslyuk
- National Research Center `Kurchatov Institute', Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
- Peter Walter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- P. Lourdu Xavier
- Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany
- Chun Hong Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Sahba Zaare
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- Viacheslav A. Ilyin
- National Research Center `Kurchatov Institute', Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
- Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- Brenda G. Hogue
- School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
- Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Ivan A. Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- DOI
- https://doi.org/10.1107/S2052252520012798
- Journal volume & issue
-
Vol. 7,
no. 6
pp. 1102 – 1113
Abstract
An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.
Keywords
