Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. The anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.

Biomedical and 10 ray Physics Department of Applied Physics AlbaNova University Center KTH Royal Institute of Technology SE 106 91 Stockholm Sweden

Center for Free Electron Laser Science DESY Notkestrasse 85 22607 Hamburg Germany

Chemical Sciences and Engineering Division Argonne National Laboratory 9700 South Cass Avenue Lemont IL 60439 USA

Condensed Matter Physics Department of Physics Chalmers University of Technology Gothenburg Sweden

Department of Physics and Astronomy Uppsala University Box 516 SE 751 20 Uppsala Sweden

Department of Physics Northwestern University 2145 Sheridan Road Evanston IL 60208 USA

Division of Scientific Computing Department of Information Technology Science for Life Laboratory Uppsala University Lagerhyddsvägen 2 SE 751 05 Uppsala Sweden

ELI Beamlines Institute of Physics Czech Academy of Science Na Slovance 2 CZ 182 21 Prague Czech Republic

European XFEL GmbH Holzkoppel 4 22869 Schenefeld Germany

Institut für Optik und Atomare Physik Technische Universität Berlin Hardenbergstr 36 10623 Berlin Germany

Laboratory of Molecular Biophysics Department of Cell and Molecular Biology Uppsala University Husargatan 3 SE 751 24 Uppsala Sweden

Linac Coherent Light Source SLAC National Accelerator Laboratory Stanford California 94309 USA

NERSC Lawrence Berkeley National Laboratory 1 Cyclotron Rd Berkeley CA 94720 USA

NSLS 2 Brookhaven National Laboratory PO Box 5000 Upton NY 11973 USA

PULSE Institute and SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA

Research Institute for Solid State Physics and Optics 1525 Budapest Hungary

University of Oxford UK

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The XBI BioLab for life science experiments at the European XFEL

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