A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking.
X-ray scattering
benchmarking standards
biomolecular small-angle scattering
neutron scattering
scattering-profile calculation
standards
Journal
Acta crystallographica. Section D, Structural biology
ISSN: 2059-7983
Titre abrégé: Acta Crystallogr D Struct Biol
Pays: United States
ID NLM: 101676043
Informations de publication
Date de publication:
01 Nov 2022
01 Nov 2022
Historique:
received:
09
07
2022
accepted:
15
09
2022
entrez:
2
11
2022
pubmed:
3
11
2022
medline:
5
11
2022
Statut:
ppublish
Résumé
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
Identifiants
pubmed: 36322416
pii: S2059798322009184
doi: 10.1107/S2059798322009184
pmc: PMC9629491
doi:
Substances chimiques
Proteins
0
Solvents
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1315-1336Subventions
Organisme : NIGMS NIH HHS
ID : P30 GM138395
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM120600
Pays : United States
Informations de copyright
open access.
Références
Curr Opin Struct Biol. 2022 Jun;74:102375
pubmed: 35490650
Nucleic Acids Res. 2015 Jul 1;43(W1):W225-30
pubmed: 25855813
J Appl Crystallogr. 2017 Jun 26;50(Pt 4):1212-1225
pubmed: 28808438
J Comput Chem. 2008 May;29(7):1019-31
pubmed: 18072177
J Am Chem Soc. 2010 Nov 10;132(44):15484-6
pubmed: 20958032
Structure. 2022 Jan 6;30(1):15-23
pubmed: 34995477
Biophys J. 1997 Jan;72(1):435-44
pubmed: 8994630
Protein Sci. 2010 Apr;19(4):642-57
pubmed: 20120026
Acta Crystallogr D Biol Crystallogr. 2010 Jun;66(Pt 6):714-24
pubmed: 20516624
J Chem Phys. 2007 Jan 7;126(1):014101
pubmed: 17212484
Acta Crystallogr D Struct Biol. 2018 Aug 1;74(Pt 8):715-726
pubmed: 30082507
Q Rev Biophys. 2003 May;36(2):147-227
pubmed: 14686102
Acta Crystallogr D Struct Biol. 2018 Dec 1;74(Pt 12):1178-1191
pubmed: 30605132
Curr Opin Struct Biol. 2019 Oct;58:197-213
pubmed: 31204190
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W184-9
pubmed: 21665925
J Synchrotron Radiat. 2014 Jan;21(Pt 1):203-8
pubmed: 24365937
Acta Crystallogr D Struct Biol. 2017 May 1;73(Pt 5):449-464
pubmed: 28471369
J Synchrotron Radiat. 2015 May;22(3):853-8
pubmed: 25931106
J Appl Crystallogr. 2015 Mar 12;48(Pt 2):431-443
pubmed: 25844078
J Mol Biol. 2004 Apr 9;337(5):1161-82
pubmed: 15046985
Acta Crystallogr D Biol Crystallogr. 2012 Oct;68(Pt 10):1278-89
pubmed: 22993082
Bioinformatics. 2003 Dec 12;19(18):2500-1
pubmed: 14668246
Biophys J. 1999 Jun;76(6):2879-86
pubmed: 10354416
J Phys Chem B. 2008 Jul 31;112(30):9020-41
pubmed: 18593145
Acta Crystallogr D Struct Biol. 2017 Sep 1;73(Pt 9):710-728
pubmed: 28876235
J Mol Biol. 1993 Feb 5;229(3):722-34
pubmed: 8381876
J Appl Crystallogr. 2016 Aug 10;49(Pt 5):1428-1432
pubmed: 27738413
J Appl Crystallogr. 2017 Sep 05;50(Pt 5):1545-1553
pubmed: 29021737
Methods Mol Biol. 2014;1091:245-58
pubmed: 24203338
Phys Chem Chem Phys. 2012 Feb 21;14(7):2483-93
pubmed: 22249363
J Am Chem Soc. 2007 May 2;129(17):5656-64
pubmed: 17411046
J Appl Crystallogr. 2013 Feb 1;46(Pt 1):1-13
pubmed: 23396808
Sci Rep. 2022 May 5;12(1):7349
pubmed: 35513443
Curr Opin Struct Biol. 2018 Apr;49:18-26
pubmed: 29172147
Biochemistry. 1988 Apr 19;27(8):2705-17
pubmed: 3401445
Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10167-72
pubmed: 8816770
BMC Res Notes. 2012 Jul 23;5:367
pubmed: 22824207
J Synchrotron Radiat. 2018 May 1;25(Pt 3):906-914
pubmed: 29714204
Curr Res Struct Biol. 2020 Aug 27;2:164-170
pubmed: 34235476
Curr Opin Struct Biol. 2016 Oct;40:1-7
pubmed: 27254833
J Chem Theory Comput. 2008 Jan;4(1):116-22
pubmed: 26619985
Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):453-62
pubmed: 14993669
J Appl Crystallogr. 2016 Oct 14;49(Pt 6):1861-1875
pubmed: 27980506
Nat Methods. 2015 May;12(5):419-22
pubmed: 25849637
J Appl Crystallogr. 2021 Feb 01;54(Pt 1):343-355
pubmed: 33833657
Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2267-72
pubmed: 9482874
Biophys J. 2014 Jul 15;107(2):435-447
pubmed: 25028885
Acta Crystallogr D Biol Crystallogr. 2015 Jan 1;71(Pt 1):57-66
pubmed: 25615860
Acta Crystallogr D Biol Crystallogr. 2006 Jul;62(Pt 7):784-92
pubmed: 16790934
J Synchrotron Radiat. 2020 Sep 1;27(Pt 5):1438-1446
pubmed: 32876621
J Appl Crystallogr. 2016 Sep 01;49(Pt 5):1827-1841
pubmed: 27738419
Proteins. 2006 Nov 15;65(3):712-25
pubmed: 16981200
J Chem Theory Comput. 2019 Aug 13;15(8):4687-4698
pubmed: 31251056
Adv Protein Chem. 1974;28:239-345
pubmed: 4598824
J Struct Biol. 2010 Jan;169(1):45-53
pubmed: 19723583
J Comput Chem. 2015 May 15;36(13):996-1007
pubmed: 25824339
Biochemistry. 1970 Mar 3;9(5):1216-23
pubmed: 5461510
Protein Sci. 2020 Jan;29(1):66-75
pubmed: 31576635
Acta Crystallogr D Biol Crystallogr. 2007 Dec;63(Pt 12):1254-68
pubmed: 18084073
Bioinformatics. 2018 Jun 1;34(11):1944-1946
pubmed: 29300836
IUCrJ. 2017 Aug 08;4(Pt 5):518-528
pubmed: 28989709
Acta Crystallogr D Struct Biol. 2016 Dec 1;72(Pt 12):1254-1266
pubmed: 27917826
J Appl Crystallogr. 2016 Nov 02;49(Pt 6):2015-2020
pubmed: 27980509
Nucleic Acids Res. 2016 Jul 8;44(W1):W424-9
pubmed: 27151198
Proteins. 2010 Jun;78(8):1950-8
pubmed: 20408171
Adv Exp Med Biol. 2017;1009:107-129
pubmed: 29218556