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

      1 , 2 , a , 2 , 3 , 4 , 3 , 3 , 5 , b , 1 , 6 , 2 , 7 , 8 , 2 , 2 , 3 , 4 , 9 , 1 , 2 , 10 , 1 , 11 , 12 , 1 , 13 , 1 , 2 , 11 , 14 , 15 , 16 , 17 , 18 , 19 , 1 , 20 , 21 , 1 , 19 , 1 , 1 , 17 , 1 , 22 , 16 , 23 , 16 , 1 , 1 , 24 , 17 , 18 , 1 , 1 , 23 , 25 , 26 , 3 , 9 , 27

      Scientific Data

      Nature Publishing Group

      X-ray tomography, Single-molecule biophysics, Virus structures, Biological physics

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          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.

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          Most cited references 16

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          Three-dimensional reconstruction of the giant mimivirus particle with an x-ray free-electron laser.

          We present a proof-of-concept three-dimensional reconstruction of the giant mimivirus particle from experimentally measured diffraction patterns from an x-ray free-electron laser. Three-dimensional imaging requires the assembly of many two-dimensional patterns into an internally consistent Fourier volume. Since each particle is randomly oriented when exposed to the x-ray pulse, relative orientations have to be retrieved from the diffraction data alone. We achieve this with a modified version of the expand, maximize and compress algorithm and validate our result using new methods.
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            Large-format, high-speed, X-ray pnCCDs combined with electron and ion imaging spectrometers in a multipurpose chamber for experiments at 4th generation light sources

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              Single particle X-ray diffractive imaging.

              In nanotechnology, strategies for the creation and manipulation of nanoparticles in the gas phase are critically important for surface modification and substrate-free characterization. Recent coherent diffractive imaging with intense femtosecond X-ray pulses has verified the capability of single-shot imaging of nanoscale objects at suboptical resolutions beyond the radiation-induced damage threshold. By intercepting electrospray-generated particles with a single 15 femtosecond soft-X-ray pulse, we demonstrate diffractive imaging of a nanoscale specimen in free flight for the first time, an important step toward imaging uncrystallized biomolecules.
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                Author and article information

                Journal
                Sci Data
                Sci Data
                Scientific Data
                Nature Publishing Group
                2052-4463
                27 June 2017
                2017
                : 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
                sdata201779
                10.1038/sdata.2017.79
                5501160
                28654088
                Copyright © 2017, The Author(s)

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files made available in this article.

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