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

doi:10.1107/S2052252520012798

An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser

IUCrJ. 2020 Oct 15;7(Pt 6):1102-1113. doi: 10.1107/S2052252520012798. eCollection 2020 Nov 1.

Authors

Dameli Assalauova¹, Young Yong Kim¹, Sergey Bobkov², Ruslan Khubbutdinov^{1

3}, Max Rose¹, Roberto Alvarez^{4

5}, Jakob Andreasson⁶, Eugeniu Balaur⁷, Alice Contreras^{8

9}, Hasan DeMirci^{10

11}, Luca Gelisio¹², Janos Hajdu^{6

13}, Mark S Hunter¹⁴, Ruslan P Kurta¹⁵, Haoyuan Li^{16

14}, Matthew McFadden⁹, Reza Nazari^{4

17}, Peter Schwander¹⁸, Anton Teslyuk^{2

19}, Peter Walter¹⁴, P Lourdu Xavier^{12

14

20}, Chun Hong Yoon¹⁴, Sahba Zaare^{4

14}, Viacheslav A Ilyin^{2

19}, Richard A Kirian⁴, Brenda G Hogue^{8

9

21}, Andrew Aquila¹⁴, Ivan A Vartanyants^{1

3}

Affiliations

¹ Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany.
² National Research Center 'Kurchatov Institute', Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation.
³ National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe sh. 31, Moscow, 115409, Russian Federation.
⁴ Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA.
⁵ School of Mathematics and Statistical Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA.
⁶ Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic.
⁷ 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.
⁸ School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA.
⁹ Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA.
¹⁰ Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
¹¹ Department of Molecular Biology and Genetics, Koc University, Istanbul, 34450, Turkey.
¹² Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany.
¹³ Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, SE-75124, Sweden.
¹⁴ SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
¹⁵ European XFEL, Holzkoppel 4, Schenefeld, D-22869, Germany.
¹⁶ Physics Department, Stanford University, 450 Jane Stanford Way, Stanford, CA 94305-2004, USA.
¹⁷ School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA.
¹⁸ University of Wisconsin Milwaukee, Milwaukee WI 53211, USA.
¹⁹ Moscow Institute of Physics and Technology, Moscow, 141700, Russian Federation.
²⁰ Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, D-22761, Germany.
²¹ Biodesign Institute, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA.

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: XFELs; bacteriophage PR772; single-particle imaging; three-dimensional virus reconstruction.

Grants and funding

This work was funded by Helmholtz Association grant HRSF-0002 to Dameli Assalauova, , , , , , , and Ivan A. Vartanyants. Russian Science Foundation grant 18-41-06001 to Dameli Assalauova, , , , , , , and Ivan A. Vartanyants. BioXFEL Science and Technology Center grant 1231306 to Hasan DeMirci and Peter Schwander. European Regional Development Fund grant . Ministerstvo Školství, Mládeže a Tělovýchovy grant . European Research Council grant ERC-2013-SyG 609920 to P. Lourdu Xavier. Human Frontier Science Program grant . Joachim Herz Stiftung grant . Vetenskapsrådet grant . Knut och Alice Wallenbergs Stiftelse grant . Röntgen-Ångström Cluster grant . Türkiye Bilimsel ve Teknolojik Araştirma Kurumu grant 118C270 to Hasan DeMirci.