Single-particle imaging without symmetry constraints at an X-ray free-electron laser

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

doi:10.1107/S205225251801120X

Single-particle imaging without symmetry constraints at an X-ray free-electron laser

IUCrJ. 2018 Sep 18;5(Pt 6):727-736. doi: 10.1107/S205225251801120X. eCollection 2018 Nov 1.

Authors

Max Rose¹, Sergey Bobkov², Kartik Ayyer³, Ruslan P Kurta⁴, Dmitry Dzhigaev¹, Young Yong Kim¹, Andrew J Morgan³, Chun Hong Yoon⁵, Daniel Westphal⁶, Johan Bielecki^{6

4}, Jonas A Sellberg^{7

6}, Garth Williams⁸, Filipe R N C Maia^{6

9}, Olexander M Yefanov³, Vyacheslav Ilyin², Adrian P Mancuso⁴, Henry N Chapman³, Brenda G Hogue^{10

11

12}, Andrew Aquila⁵, Anton Barty³, Ivan A Vartanyants^{1

13}

Affiliations

¹ Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg D-22607, Germany.
² National Research Centre 'Kurchatov Institute', Akademika Kurchatova pl. 1, Moscow 123182, Russia.
³ Center for Free Electron Laser Science (CFEL), Notkestrasse 85, Hamburg 22607, Germany.
⁴ European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany.
⁵ Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
⁶ Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Sweden.
⁷ Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm SE-106 91, Sweden.
⁸ Brookhaven National Laboratory, 98 Rochester St, Shirley, NY 11967, USA.
⁹ NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹⁰ Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, Biodesign Institute at Arizona State University, Tempe 85287, USA.
¹¹ Biodesign Center for Applied Structural Discovery, Biodesign Institute at Arizona State University, Tempe, AZ 85287, USA.
¹² Arizona State University, School of Life Sciences (SOLS), Tempe, AZ 85287, USA.
¹³ National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe shosse 31, Moscow 115409, Russia.

Abstract

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.

Keywords: XFELs; single-particle imaging; three-dimensional virus reconstructions.

Grants and funding

This work was funded by U.S. Department of Energy, Office of Science grant DE-AC02-76SF00515. Helmholtz Association, Initiative and Networking fund grant . Russian Science Foundation grant 18-41-06001. Joachim Herz Stiftung grant . Vetenskapsrådet grant . Stiftelsen för Strategisk Forskning grant . National Science Foundation, Science and Technology Center grant 1231306.