Crystallographic model quality at a glance
Open accessAbstract
A crystallographic macromolecular model is typically characterized by a list of quality criteria, such as R factors, deviations from ideal stereochemistry and average B factors, which are usually provided as tables in publications or in structural databases. In order to facilitate a quick model-quality evaluation, a graphical representation is proposed. Each key parameter such as R factor or bond-length deviation from ;ideal values' is shown graphically as a point on a ;ruler'. These rulers are plotted as a set of lines with the same origin, forming a hub and spokes. Different parts of the rulers are coloured differently to reflect the frequency (red for a low frequency, blue for a high frequency) with which the corresponding values are observed in a reference set of structures determined previously. The points for a given model marked on these lines are connected to form a polygon. A polygon that is strongly compressed or dilated along some axes reveals unusually low or high values of the corresponding characteristics. Polygon vertices in ;red zones' indicate parameters which lie outside typical values.
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The R values of the refined structures are well within the range that is typical at the corresponding resolutions.
“The R values of the refined structures (Extended Data Table 1) are well within the range that is typical at the corresponding resolutions74.”
From Architecture of the synaptotagmin–SNARE machinery for neuronal exocytosis (2015) · cites this paper as [74]
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Cited by
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<i>PHENIX</i> : a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716 · see citing works
Self-citationTowards automated crystallographic structure refinement with <i>phenix.refine</i>
Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H., & Adams, P. D. (2012) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444912001308 · Cited by 5,511 · see citing works
Self-citationArchitecture of the synaptotagmin–SNARE machinery for neuronal exocytosis
Zhou, Q., Lai, Y., Bacaj, T., Zhao, M., Lyubimov, A. Y., Uervirojnangkoorn, M., Zeldin, O. B., Brewster, A. S., Sauter, N. K., Cohen, A. E., et al. (2015) · Nature · doi:10.1038/nature14975 · Cited by 348 · see citing works
- Authors
- Urzhumtseva, L., Afonine, P. V., Adams, P. D., & Urzhumtsev, A.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Lawrence Berkeley National Laboratory (US)
- Corresponding author
- Urzhumtsev, Alexandre
- Venue
- Acta Crystallographica Section D Biological Crystallography
- Published
- 2009-02-20
- Volume
- 65
- Issue
- 3
- Pages
- 297-300
- ISSN
- 0907-4449 (ISSN-L)
- PMC
- PMC2651759
- OpenAlex
- W2139042077
- Cited by
- 110
- References
- 0
- Citations by year
- 2026: 4 · 2025: 2 · 2024: 5 · 2023: 2 · 2022: 4 · 2021: 6 · 2020: 7 · 2019: 5 · 2018: 9 · 2017: 5 · 2016: 8 · 2015: 16 · 2014: 6 · 2013: 13 · 2012: 4
- FWCI
- 2.90
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Acta Crystallographica Section D Biological Crystallography (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- HAL (submittedVersion)
- Funders
- National Institute of General Medical Sciences (P01GM063210)
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Inorganic Chemistry › Crystal structures of chemical compounds
- Keywords
- R-factor, stereochemistry, Debye-Waller factor
- MeSH terms
- Algorithms, Computer Graphics, Models, Molecular, Molecular Conformation, Stereoisomerism, Crystallography, X-Ray, Macromolecular Substances, Validation Studies as Topic
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