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

Trewhella, Jill; Vachette, Patrice; Bierma, Jan; Blanchet, Clement; Brookes, Emre; Chakravarthy, Srinivas; Chatzimagas, Leonie; Cleveland, IV, Thomas E.; Cowieson, Nathan; Crossett, Ben; Duff, Anthony P.; Franke, Daniel; Gabel, Frank; Gillilan, Richard E.; Graewert, Melissa; Grishaev, Alexander; Guss, J. Mitchell; Hammel, Michal; Hopkins, Jesse; Huang, Qingqui; Hub, Jochen S.; Hura, Greg L.; Irving, Thomas C.; Jeffries, Cy Michael; Jeong, Cheol; Kirby, Nigel; Krueger, Susan; Martel, Anne; Matsui, Tsutomu; Li, Na; Pérez, Javier; Porcar, Lionel; Prangé, Thierry; Rajkovic, Ivan; Rocco, Mattia; Rosenberg, Daniel J.; Ryan, Timothy M.; Seifert, Soenke; Sekiguchi, Hiroshi; Svergun, Dmitri; Teixeira, Susana; Thureau, Aurelien; Weiss, Thomas M.; Whitten, Andrew E.; Wood, Kathleen; Zuo, Xiaobing

doi:10.1107/s2059798322009184

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

Journal Article · Thu Oct 20 00:00:00 EDT 2022 · Acta Crystallographica. Section D. Structural Biology

DOI:https://doi.org/10.1107/s2059798322009184· OSTI ID:1894167

^[1]; ^[2]; Bierma, Jan ^[3]; ^[4]; Brookes, Emre ^[5]; Chakravarthy, Srinivas ^[6]; ^[7]; Cleveland, IV, Thomas E. ^[8]; ^[9]; ^[1]; ^[10]; Franke, Daniel ^[4]; ^[11]; ^[12]; ^[4]; Grishaev, Alexander ^[8]; ^[1]; Hammel, Michal ^[3]; ^[6]; Huang, Qingqui ^[12] more »

Univ. of Sydney, NSW (Australia)
Alternative Energies and Atomic Energy Commission (CEA), Paris (France); Centre National de la Recherche Scientifique (CNRS) (France); Univ. Paris-Saclay, Gif-sur-Yvette (France)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
European Molecular Biology Laboratory (EMBL), Grenoble (France)
Univ. of Montana, Missoula, MT (United States)
Illinois Institute of Technology, Chicago, IL (United States)
Saarland University Campus, Saarbrücken (Germany)
Institute for Bioscience and Biotechnology Research, Rockville, MD (United States); National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States)
Science and Technology Facilities Council (STFC), Oxford (United Kingdom). Diamond Light Source, Ltd.
Australian Nuclear Science and Technology Organisation, NSW (Australia)
Univ. of Grenoble Alpes, Grenoble (France); Alternative Energies and Atomic Energy Commission (CEA), Grenoble (France); Centre National de la Recherche Scientifique (CNRS) (France)
Cornell Univ., Ithaca, NY (United States). Cornell High Energy Synchrotron Source (CHESS)
Indiana Wesleyan Univ., Marion, IN (United States)
Australian Nuclear Science and Technology Organisation (ANSTO), Melbourne, VIC (Australia). Australian Synchrotron
National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States)
Inst. Laue-Langevin (ILL), Grenoble (France)
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
Chinese Academy of Sciences (CAS) (China). Shanghai Advanced Research Institute. National Facility for Protein Science in Shanghai
Synchrotron SOLEIL, Gif-sur-Yvette (France)
Centre National de la Recherche Scientifique-Mixed Organizations (CNRS-UMR), Paris (France)
Proteomica e Spettrometria di Massa, IRCCS Ospedale Policlinico San Martino, Genova (Italy)
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
SPring-8, Japan Synchrotron Radiation Research Institute (JSRRI), Sayo (Japan)
Univ. of Delaware, Newark, DE (United States); National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States)

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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); Bundesministerium für Bildung und Forschung (BMBF); National Institutes of Health (NIH); National Science Foundation (NSF); German Research Foundation (DFG); US Department of Commerce; National Natural Science Foundation of China (NSFC); Natural Science Foundation of Shanghai; USDOE

Grant/Contract Number:: AC02-05CH11231; AC02-06CH11357; AC02-76SF00515; 70NANB2oH133; GM120600; GM138395; IS10OD018090; S10OD021512; P30GM133894; 1-P30- GM124166-01A1; 1912444; DMR-2010792; DMR-1829070; HU 1971/3-1; 16QK10A; U1832144; 21ZR1471600

OSTI ID:: 1894167

Alternate ID(s):: OSTI ID: 1992078; OSTI ID: 2404305

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Vol. 78, Issue 11; ISSN 2059-7983

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

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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

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