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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dc.contributor.authorTrewhella, Jen_AU
dc.contributor.authorVachette, Pen_AU
dc.contributor.authorBierma, Jen_AU
dc.contributor.authorBlanchet, Clen_AU
dc.contributor.authorBrookes, Een_AU
dc.contributor.authorChakravarthy, Sen_AU
dc.contributor.authorChatzimagas, Len_AU
dc.contributor.authorCleveland, TEen_AU
dc.contributor.authorCowieson, NPen_AU
dc.contributor.authorCrossett, Ben_AU
dc.contributor.authorDuff, APen_AU
dc.contributor.authorFranke, Den_AU
dc.contributor.authorGabel, Fen_AU
dc.contributor.authorGillilan, REen_AU
dc.contributor.authorGraewert, MAen_AU
dc.contributor.authorGrishaev, Aen_AU
dc.contributor.authorGuss, JMen_AU
dc.contributor.authorHammel, Men_AU
dc.contributor.authorHopkins, JBen_AU
dc.contributor.authorHuang, Qen_AU
dc.contributor.authorHub, JSen_AU
dc.contributor.authorHura, GLen_AU
dc.contributor.authorIrving, TCen_AU
dc.contributor.authorJeffries, CMen_AU
dc.contributor.authorJeong, Cen_AU
dc.contributor.authorKirby, Nen_AU
dc.contributor.authorKrueger, Sen_AU
dc.contributor.authorMartel, Aen_AU
dc.contributor.authorMatsui, Ten_AU
dc.contributor.authorLi, Nen_AU
dc.contributor.authorPérez, Jen_AU
dc.contributor.authorPorcar, Len_AU
dc.contributor.authorPrangé, Ten_AU
dc.contributor.authorRajkovic, Ien_AU
dc.contributor.authorRocco, Men_AU
dc.contributor.authorRosenberg, DJen_AU
dc.contributor.authorRyan, TMen_AU
dc.contributor.authorSeifert, Sen_AU
dc.contributor.authorSekiguchi, Hen_AU
dc.contributor.authorSvergun, Den_AU
dc.contributor.authorTeixeira, Sen_AU
dc.contributor.authorThureau, Aen_AU
dc.contributor.authorWeiss, TMen_AU
dc.contributor.authorWhitten, AEen_AU
dc.contributor.authorWood, Ken_AU
dc.contributor.authorZuo, Xen_AU
dc.date.accessioned2025-01-09T20:59:38Zen_AU
dc.date.available2025-01-09T20:59:38Zen_AU
dc.date.issued2022-11en_AU
dc.date.statistics2024-11-05en_AU
dc.description.abstractThrough 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. © The Authors published by International Union of Crystallography. Open Access CC-By licence 4.0.en_AU
dc.description.sponsorshipANSTO supported the provision of beamtime on the Quokka SANS instrument (Proposal No. 8038). Shipping costs for this project were donated by the Australian Synchrotron, ANSTO. Sample preparation was supported under proposal NDF8018 at the National Deuteration Facility, which is partly supported by the National Collaborative Research Infrastructure Strategy, an initiative of the Australian Government. The experiments on BL40B2 at SPring-8 were performed with the approval of the Japan Synchrotron Radiation Research Institute (JASRI; Proposal No. 2019A2059). ALS SIBYLS data collection was made possible by Department of Energy Integrated Diffraction Analysis Technologies (IDAT) program. We thank Sanofi–Aventis for the gift of urate oxidase and Professor H. van Tilbeurgh (I2BC, Gif-sur-Yvette, France) for shipping costs. Thanks to Paul Butler for helpful discussions regarding SANS and resolution-smearing corrections. JP and AT thank Blandine Pineau for all dialyses performed for the SWING beamline. Sample preparation for ILL SANS measurements was supported by the ILL chemistry laboratory (M. Sandroni). Certain commercial equipment, materials, software or suppliers are identified in this paper to foster understanding. Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the materials or equipment identified are necessarily the best available for the purpose. The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH. Author contributions were as follows. JT and PV oversaw the planning and coordinated the project, performed extensive data analysis and validation, developed the consensus data, made comparisons with prediction and prepared the first draft manuscript. DF developed the datcombine tool and contributed the text describing the tool. JH and LC performed the WAXSiS calculations for SAXS and SANS in H2O and D2O to the extended q of 1 Å−1 for all proteins and contributed the detailed descriptions. TP produced and purified the urate oxidase samples. CB, JB, SC, NC, RG, MG, AG, MH, QH, JH, GH, TI, CMJ, NK, TM, NL, JP, IR, DJR, TR, MS, HS, DS, SS, AT, TW and XZ collected SAXS data and/or consulted on experiment/analysis details. PB, TEC, FG, LP, SK, AM, ST, AEW and KW collected SANS data and/or consulted on experiment/analysis details. BC provided mass-spectrometry data, analysis and interpretation. AD, TP, TR and PV prepared samples/buffers, characterized samples for shipment and arranged international shipping. EB and CJ are developing the Multi-SAXS Hub. EB, MR and PV provided the derivation of VP/m and the calculations for specific proteins. JMG and MR provided input on the original project concept and plan. All authors reviewed, commented on and approved the original project plan and submitted the manuscript. Open access publishing facilitated by The University of Sydney, as part of the Wiley - The University of Sydney agreement via the Council of Australian University Librarians. Funding for this research was provided by: National Institutes of Health, National Institute of General Medical Sciences (grant No. GM120600 to Emre Brookes; grant No. GM138395 to Thomas C. Irving; grant No. IS10OD018090 to Thomas C. Irving; grant No. S10OD021512 to William Weiss; grant No. P30GM133894 to Keith O. Hodgson; grant No. 1-P30-GM124166-01A1 to Richard E. Gillilan); National Science Foundation (grant No. 1912444 to Emre Brookes; grant No. DMR-2010792 to Dan Neumann; grant No. DMR-1829070 to Richard E. Gillilan); Deutsche Forschungsgemeinschaft (grant No. HU 1971/3-1 to Jochen S. Hub); US Department of Energy (contract No. DE-AC02-06CH11357; contract No. DE-AC02-76SF00515); Horizon 2020 Framework Programme (grant No. 871037 to Dmitri Svergun); Bundesministerium für Bildung und Forschung (grant No. 16QK10A to Dmitri Svergun); US Department of Commerce (award No. 70NANB2oH133 to Norman Wagner, Paramita Mondal, Susana Teixeira); National Natural Science Foundation of China (grant No. U1832144 to Na Li); Natural Science Foundation of Shanghai (grant No. 21ZR1471600 to Na Li).en_AU
dc.format.mediumPrint-Electronicen_AU
dc.identifier.citationTrewhella, J., Vachette, P., Bierma, J., Blanchet, C., Brookes, E., Chakravarthy, S., Chatzimagas, L., Cleveland, T. E., IV, Cowieson, N., Crossett, B., Duff, A. P., Franke, D., Gabel, F., Gillilan, R. E., Graewert, M., Grishaev, A., Guss, J. M., Hammel, M., Hopkins, J., Huang, Q., Hub, J., Hura, G. L., Irving, T. C., Jeffries, C. M., Jeong, C., Kirby, N., Krueger, S., Martel, A., Matsui, T., Li, N., Perez, J., Procar, L., Prange, T., Rajikovic, I., Rocco, M., Rosenberg, D. J., Ryan, T. M., Seifert, S., Sekiguchi, H., Svergun, D., Teixeira, S., Thureau, A., Weiss, T. M., Whitten, A. E., Wood, K., & Zuo, X. (2022). A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking. Acta Crystallographica Section D, 78(11), 1315-1336. doi:10.1107/S2059798322009184en_AU
dc.identifier.issn2059-7983en_AU
dc.identifier.issue11en_AU
dc.identifier.journaltitleActa Crystallographica Section D, Structural Biologyen_AU
dc.identifier.pagination1315-1336en_AU
dc.identifier.urihttps://doi.org/10.1107/s2059798322009184en_AU
dc.identifier.urihttps://apo.ansto.gov.au/handle/10238/15873en_AU
dc.identifier.volume78en_AU
dc.languageengen_AU
dc.language.isoenen_AU
dc.publisherInternational Union of Crystallography (IUCr)en_AU
dc.subjectNeutron diffractionen_AU
dc.subjectStandardsen_AU
dc.subjectX-ray diffractionen_AU
dc.subjectScatteringen_AU
dc.subjectMoleculesen_AU
dc.subjectSmall angle scatteringen_AU
dc.subjectSmall angle scatteringen_AU
dc.subjectBenchmarksen_AU
dc.titleA round‐robin approach provides a detailed assessment of biomolecular small‐angle scattering data reproducibility and yields consensus curves for benchmarkingen_AU
dc.typeJournal Articleen_AU
dcterms.dateAccepted2022-09-15en_AU
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