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Accurate assessment of mass, models and resolution by small-angle scattering
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Modern small-angle scattering (SAS) experiments with X-rays or neutrons provide a comprehensive, resolution-limited observation of the thermodynamic state. However, methods for evaluating mass and validating SAS-based models and resolution have been inadequate. Here we define the volume of correlation, Vc, a SAS invariant derived from the scattered intensities that is specific to the structural state of the particle, but independent of concentration and the requirements of a compact, folded particle. We show that Vc defines a ratio, QR, that determines the molecular mass of proteins or RNA ranging from 10 to 1,000 kilodaltons. Furthermore, we propose a statistically robust method for assessing model-data agreements (χ(2)free) akin to cross-validation. Our approach prevents over-fitting of the SAS data and can be used with a newly defined metric, RSAS, for quantitative evaluation of resolution. Together, these metrics (Vc, QR, χ(2)free and RSAS) provide analytical tools for unbiased and accurate macromolecular structural characterizations in solution.
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“additional strategies such as the combination of Vc, Qr, X2free, and Rsas metrics have been proposed as more robust evaluation metrics75.”
From The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins (2024) · cites this paper as [75]
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Metadata
- Authors
- Rambo, R. P., & Tainer, J. A.
- Affiliations
- Lawrence Berkeley National Laboratory (US)
- Scripps Research Institute (US)
- Corresponding author
- Rambo, Robert P.
- Tainer, John A.
- Venue
- Nature
- Published
- 2013-04
- Volume
- 496
- Issue
- 7446
- Pages
- 477-481
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3714217
- OpenAlex
- W1984084102
- Cited by
- 750
- References
- 35
- Citations by year
- 2026: 34 · 2025: 34 · 2024: 39 · 2023: 46 · 2022: 81 · 2021: 57 · 2020: 71 · 2019: 65 · 2018: 64 · 2017: 70 · 2016: 74 · 2015: 53 · 2014: 43 · 2013: 19
- FWCI
- 28.41
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Cancer Institute (R35CA220430)
- National Institute of General Medical Sciences (R01GM105404)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Physics and Astronomy › Radiation › Nuclear Physics and Applications
- Keywords
- small-angle scattering, molecular mass estimation, model-data agreement, resolution assessment, model validation, protein complexes, macromolecular flexibility, solution structure
- MeSH terms
- DNA-Binding Proteins, Models, Chemical, Models, Molecular, Molecular Conformation, Molecular Weight, RNA, Viral, Solutions, Reproducibility of Results, RNA-Binding Proteins, Pliability, Aldose-Ketose Isomerases, Scattering, Small Angle, Riboswitch
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