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A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking

DOI: 10.1107/S2059798322009184 DOI Help

Authors: Jill Trewhella (The University of Sydney) , Patrice Vachette (Université Paris-Saclay, CEA, CNRS) , Jan Bierma (Lawrence Berkeley National Laboratory) , Clement Blanchet (European Molecular Biology Laboratory (EMBL) Hamburg Unit) , Emre Brookes (The University of Sydney) , Srinivas Chakravarthy (Illinois Institute of Technology) , Leonie Chatzimagas (Saarland University) , Thomas E. Cleveland (Institute for Bioscience and Biotechnology Research; National Institute of Standards and Technology) , Nathan Cowieson (Diamond Light Source) , Ben Crossett (The University of Sydney) , Anthony P. Duff (Institute for Bioscience and Biotechnology Research; National Institute of Standards and Technology) , Daniel Franke (European Molecular Biology Laboratory (EMBL) Hamburg Unit) , Frank Gabel (CEA, CNRS, Université Grenoblé Alpes) , Richard E. Gillilan (Cornell High-Energy Synchrotron Source) , Melissa Graewert (European Molecular Biology Laboratory (EMBL) Hamburg Unit) , Alexander Grishaev (Institute for Bioscience and Biotechnology Research; National Institute of Standards and Technology) , J. Mitchell Guss (The University of Sydney) , Michal Hammel (Lawrence Berkeley National Laboratory) , Jesse Hopkins (Illinois Institute of Technology) , Qingqui Huang (Cornell High-Energy Synchrotron Source) , Jochen S. Hub (Saarland University) , Greg L. Hura (Lawrence Berkeley National Laboratory) , Thomas C. Irving (Illinois Institute of Technology) , Cy Michael Jeffries (European Molecular Biology Laboratory (EMBL) Hamburg Unit) , Cheol Jeong (Wesleyan University) , Nigel Kirby (Australian Synchrotron) , Susan Krueger (National Institute of Standards and Technology) , Anne Martel (Institut Laue–Langevin) , Tsutomu Matsui (Stanford Synchrotron Radiation Lightsource) , Na Li (Shanghai Advanced Research Institute) , Javier Pérez (Synchrotron SOLEIL) , Lionel Porcar (Institut Laue–Langevin) , Thierry Prange (CITCoM (UMR 8038 CNRS)) , Ivan Rajkovic (Stanford Synchrotron Radiation Lightsource) , Mattia Rocco (IRCCS Ospedale Policlinico San Martino) , Daniel J. Rosenberg (Lawrence Berkeley National Laboratory) , Timothy M. Ryan (Australian Synchrotron) , Soenke Seifert (Advanced Photon Source) , Hiroshi Sekiguchi (SPring-8, Japan Synchrotron Radiation Research Institute) , Dmitri Svergun (European Molecular Biology Laboratory (EMBL) Hamburg Unit) , Susana Teixeira (National Institute of Standards and Technology; University of Delaware) , Aurelien Thureau (Synchrotron SOLEIL) , Thomas M. Weiss (Stanford Synchrotron Radiation Lightsource) , Andrew E. Whitten (Australian Nuclear Science and Technology Organisation) , Kathleen Wood (Australian Nuclear Science and Technology Organisation) , Xiaobing Zuo (Advanced Photon Source)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Acta Crystallographica Section D Structural Biology , VOL 78

State: Published (Approved)
Published: November 2022

Open Access Open Access

Abstract: Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0–1 Å−1 are consistent with theoretical prediction. The inherently lower statistical precision for SANS limited the reliably measured q-range to <0.5 Å−1, but within the limits of experimental uncertainties the major features of the consensus SANS data were also consistent with prediction for all five proteins measured in H2O and in D2O. Thus, a foundation set of consensus SAS profiles has been obtained for benchmarking scattering-profile prediction from atomic coordinates. Additionally, two sets of SAXS data measured at different facilities to q > 2.2 Å−1 showed good mutual agreement, affirming that this region has interpretable features for structural modelling. SAS measurements with inline size-exclusion chromatography (SEC) proved to be generally superior for eliminating sample heterogeneity, but with unavoidable sample dilution during column elution, while batch SAS data collected at higher concentrations and for longer times provided superior statistical precision. Careful merging of data measured using inline SEC and batch modes, or low- and high-concentration data from batch measurements, was successful in eliminating small amounts of aggregate or interparticle interference from the scattering while providing improved statistical precision overall for the benchmarking data set.

Journal Keywords: biomolecular small-angle scattering; X-ray scattering; neutron scattering; standards; benchmarking standards; scattering-profile calculation

Subject Areas: Biology and Bio-materials, Technique Development

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Added On: 25/10/2022 09:14


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Technique Development - Life Sciences & Biotech Structural biology Life Sciences & Biotech

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