COVID-19.рф: ИНФОРМАЦИЯ ПРОТИВ ПАНДЕМИИ

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Статья

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

D. Assalauova, Y. Kim, S. Bobkov, R. Khubbutdinov, M. Rose, R. Alvarez, J. Andreasson, E. Balaur, A. Contreras, H. DeMirci, L. Gelisio, J. Hajdu, M. Hunter, R. Kurta, H. Li, M. McFadden, R. Nazari, P. Schwander, A. Teslyuk, P. Walter, P. Xavier, C. Yoon, S. Zaare, V. Ilyin, R. Kirian, B. Hogue, A. Aquila, I. Vartanyants,
2020
https://doi.org/10.1107/s2052252520012798

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.

Цитирование

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Версии

  • 1. Version of Record от 2020-10-15

Метаданные

Об авторах
  • D. Assalauova
    Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany.
  • Y. Kim
    Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany.
  • S. Bobkov
    National Research Center 'Kurchatov Institute', Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation.
  • R. Khubbutdinov
    Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany., National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe sh. 31, Moscow, 115409, Russian Federation.
  • M. Rose
    Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany.
  • R. Alvarez
    Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA., School of Mathematics and Statistical Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA.
  • J. Andreasson
    Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic.
  • E. 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.
  • A. Contreras
    School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA., Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA.
  • H. DeMirci
    Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA., Department of Molecular Biology and Genetics, Koc University, Istanbul, 34450, Turkey.
  • L. Gelisio
    Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany.
  • J. Hajdu
    Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic., Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, SE-75124, Sweden.
  • M. Hunter
    SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
  • R. Kurta
    European XFEL, Holzkoppel 4, Schenefeld, D-22869, Germany.
  • H. Li
    Physics Department, Stanford University, 450 Jane Stanford Way, Stanford, CA 94305-2004, USA., SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
  • M. McFadden
    Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA.
  • R. Nazari
    Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA., School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA.
  • P. Schwander
    University of Wisconsin Milwaukee, Milwaukee WI 53211, USA.
  • A. Teslyuk
    National Research Center 'Kurchatov Institute', Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation., Moscow Institute of Physics and Technology, Moscow, 141700, Russian Federation.
  • P. Walter
    SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
  • P. Xavier
    Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany., SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA., Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, D-22761, Germany.
  • C. Yoon
    SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
  • S. Zaare
    Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA., SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
  • V. Ilyin
    National Research Center 'Kurchatov Institute', Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation., Moscow Institute of Physics and Technology, Moscow, 141700, Russian Federation.
  • R. Kirian
    Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA.
  • B. Hogue
    School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA., Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA., Biodesign Institute, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA.
  • A. Aquila
    SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
  • I. Vartanyants
    Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany., National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe sh. 31, Moscow, 115409, Russian Federation.
Название журнала
  • IUCrJ
Том
  • 7
Выпуск
  • Pt 6
Страницы
  • 1102-1113
Издатель
  • International Union of Crystallography (IUCr)
Тип документа
  • journal article
Тип лицензии Creative Commons
  • CC BY
Правовой статус документа
  • Свободная лицензия
Источник
  • dimensions
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