Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

Abstract

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.

Journal

Journal ID (nlm-ta): Sci Data

Journal ID (iso-abbrev): Sci Data

Title: Scientific Data

Publisher: Nature Publishing Group

ISSN (Electronic): 2052-4463

Publication date (Electronic): 27 June 2017

Publication date Collection: 2017

Volume: 4

Affiliations

[1 ]Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University , Husargatan 3 (Box 596), Uppsala SE-75124, Sweden

[2 ]SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA

[3 ]Center for Free-Electron Laser Science, DESY , Notkestrasse 85, 22607 Hamburg, Germany

[4 ]Centre for Ultrafast Imaging, University of Hamburg , Luruper Chaussee 149, 22761 Hamburg, Germany

[5 ]Australian Research Council Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University , Melbourne 3086, Australia

[6 ]National Research Centre ‘Kurchatov Institute’ , Akademika Kurchatova pl. 1, 123182 Moscow, Russia

[7 ]Argonne National Laboratory , 9700 S. Cass Ave, Lemont, Illinois 60439, USA

[8 ]Institut für Optik und Atomare Physik, Technische Universität Berlin , Hardenbergstraße 36, 10623 Berlin, Germany

[9 ]Department of Physics, University of Hamburg , Luruper Chausee 149, 22761 Hamburg, Germany

[10 ]Stanford PULSE Institute, SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA

[11 ]Biodesign Center for Applied Structural Discovery, Biodesign Institute at Arizona State University , Tempe, Arizona 85287-5001, USA

[12 ]School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, USA

[13 ]Institute of Physics AS CR , v.v.i., Na Slovance 2, 18221 Prague 8, Czech Republic

[14 ]Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, Biodesign Institute at Arizona State University , Tempe, Arizona 85287, USA

[15 ]Arizona State University, School of Life Sciences (SOLS) , Tempe, Arizona 85287-5401, USA

[16 ]Department of Physics, University of Wisconsin Milwaukee, KIRC , 3135 N. Maryland Ave, Milwaukee, Wisconsin 53211, USA

[17 ]Department of Physics, Pohang University of Science and Technology , Pohang 37673, Korea

[18 ]Department of Physics, Arizona State University , Tempe, Arizona 85287, USA

[19 ]European X-ray Free Electron Laser GmbH , Holzkoppel 4, 22869 Schenefeld, Germany

[20 ]Department of Physics, National University of Singapore Blk S12 , 2 Science Drive 3, Singapore 117551

[21 ]Centre for Bio-imaging Sciences, National University of Singapore Blk S1A , 14 Science Drive 4, Singapore 117557

[22 ]Division of Scientific Computing, Department of Information Technology, Science for Life Laboratory, Uppsala University , Husargatan 3 (Box 337), Uppsala SE-75105, Sweden

[23 ]Deutsches Elektronen-Synchrotron DESY , Notkestraße 85, D-22607 Hamburg, Germany

[24 ]Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology , Stockholm SE-106 91, Sweden

[25 ]National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) , Kashirskoe shosse 31, 115409 Moscow, Russia

[26 ]NSLS-II, Brookhaven National Laboratory , Upton, New York 11873, USA

[27 ]Max-Planck Institute for the Structure and Dynamics of Matter , 22607 Hamburg, Germany

Author notes

[a ] A.A. (email: Aquila@ 123456slac.stanford.ed )

[b ] J.B. (email: johanb@ 123456xray.bmc.uu.se )

[†]

Present address: California Lutheran University, 60 Olsen Road, Thousand Oaks, California 91360, USA

[]

A.A., A.B., A.Ma., A.Mu., B.H., C.S., D.N., G.C., G.V.D.S., H.D., J.A.S., K.A., M.B., M.F.H., M.Se., M.Sv., N.D.L., P.B., R.A.K., S.A., and Y.K.: Instrument alignment and data collection. A.B., A.O., C.H.Y., C.N., G.V.D.S., I.A.V., J.A.S., K.A., M.F.H., M.R., N.D.L., P.S., R.K., and S.B.: Data analysis. J.B., J.C.H.S., J.H., K.M., M.Sv., and P.B.: Injector Development. A.Mu., B.H., K.M., M.Sv., P.F., and P.L.X.: Sample characterization & Preparation. D.L., H.C., and M.B.: Instrumentation Development. C.H.Y., G.C., P.H., and S.C.: Detector Operations and development. A.B., A.O., B.D., C.H.Y., C.N., F.R.N.C.M., G.V.D.S., K.A., M.F.H., N.D.L., P.S.: Software development.

Article

Publisher Item ID: sdata201779

DOI: 10.1038/sdata.2017.79

PMC ID: 5501160

PubMed ID: 28654088

Copyright statement: Copyright © 2017, The Author(s)

License:

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Categories

Subject: Data Descriptor