Linking Crystallographic Model and Data Quality
Open accessAbstract
Finessing Crystal Analysis: Protein crystallography has revolutionized our understanding of a whole variety of biological processes (see the Perspective by Evans ). In crystallography, the measure of agreement between the data and the calculated model is not on the same scale as the measure of data quality, making it challenging to choose an optimal high resolution limit beyond which the data should be discarded. Now, Karplus and Diederichs (p. 1030 ) introduce a statistical model that assesses agreement of model and data accuracy on the same scale. Determining the structures of biological macromolecules by x-ray crystallography requires solving the phase problem. The two techniques that dominate phase evaluation (multi- and single-wavelength anomalous diffraction) rely on element-specific scattering from incorporated heavy atoms. Liu et al. (p. 1033 ) present procedures for routine structure determination of native proteins with no heavy atom incorporation. The technique, which relies on combining data from multiple crystals, was used to determine the structures of four native proteins, including a 1200-residue complex.
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The final resolution for the TrkA-minibinder data was selected as 1.84 Å by comparing paired refinements at 1.84, 1.90, 1.95, 2.00 and 2.05 Å.
“The final resolution of the data was selected as 1.84 Å by comparing the results of paired refinements at 1.84, 1.90, 1.95, 2.00 and 2.05 Å resolution70.”
From Design of protein-binding proteins from the target structure alone (2022) · cites this paper as [70]
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Cites
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works
<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
Kabsch, W. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909047337 · Cited by 16,463 · see citing works
Overview of the <i>CCP</i> 4 suite and current developments
Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., et al. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910045749 · Cited by 12,353 · see citing works
Statistical Methods for Research Workers
Fisher, R. A. (1945) · American Journal of Clinical Pathology · doi:10.1093/ajcp/15.11.552b · Cited by 10,883 · see citing works
Scaling and assessment of data quality
Evans, P. (2005) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444905036693 · Cited by 4,391 · see citing works
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
Brünger, A. T. (1992) · Nature · doi:10.1038/355472a0 · Cited by 3,877 · see citing works
Integration, scaling, space-group assignment and post-refinement
Kabsch, W. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909047374 · Cited by 2,494 · see citing works
Rosenthal, P. B., & Henderson, R. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.07.013 · Cited by 2,416 · see citing works
Substructure solution withSHELXD
Schneider, T. R., & Sheldrick, G. M. (2002) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444902011678 · Cited by 1,591 · see citing works
An introduction to data reduction: space-group determination, scaling and intensity statistics
Evans, P. R. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s090744491003982x · Cited by 1,507 · see citing works
Improved R-factors for diffraction data analysis in macromolecular crystallography
Diederichs, K., & Karplus, P. A. (1997) · Nature Structural Biology · doi:10.1038/nsb0497-269 · Cited by 841 · see citing works
Self-citationGlobal indicators of X-ray data quality
Weiss, M. S. (2001) · Journal of Applied Crystallography · doi:10.1107/s0021889800018227 · Cited by 702 · see citing works
Remarks about protein structure precision
Cruickshank, D. W. J. (1999) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998012645 · Cited by 484 · see citing works
Crystal Structure of Mammalian Cysteine Dioxygenase
Simmons, C. R., Liu, Q., Huang, Q., et al. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m601555200 · Cited by 179 · see citing works
A Course in Theortical Statistics.
Blackmor, R. W., & Rahman, N. A. (1970) · Journal of the Royal Statistical Society Series D (The Statistician) · doi:10.2307/2987374 · Cited by 153 · see citing works
Correlation and Regression: Applications for Industrial Organizational Psychology and Management
Bobko, P. (2001) · Cited by 121 · see citing works
Prediction, Parsimony and Noise
Gauch, H. G. (1993) · Cited by 113 · see citing works
A Putative Fe 2+ -Bound Persulfenate Intermediate in Cysteine Dioxygenase
Simmons, C. R., Krishnamoorthy, K., Granett, S. L., et al. (2008) · Biochemistry · doi:10.1021/bi801546n · Cited by 97 · see citing works
Luzzati, V. (1953) · Acta Crystallographica · doi:10.1107/s0365110x53000508 · Cited by 87 · see citing works
Re-refinement from deposited X-ray data can deliver improved models for most PDB entries
Joosten, R. P., Womack, T., Vriend, G., et al. (2009) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444908037591 · Cited by 80 · see citing works
A computer-linked cathode-ray tube microdensitometer for X-ray crystallography
Arndt, U. W., Crowther, R. A., & Mallett, J. F. W. (1968) · Journal of Physics E Scientific Instruments · doi:10.1088/0022-3735/1/5/303 · Cited by 78 · see citing works
Largest likely values for the reliability index
Wilson, A. J. C. (1950) · Acta Crystallographica · doi:10.1107/s0365110x50001129 · Cited by 68 · see citing works
Fisher's information in maximum-likelihood macromolecular crystallographic refinement
Steiner, R. A., Lebedev, A. A., & Murshudov, G. N. (2003) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444903018675 · Cited by 62 · see citing works
Inclusion of weak high-resolution X-ray data for improvement of a group II intron structure
Wang, J. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910029938 · Cited by 27 · see citing works
Simulation of X-ray frames from macromolecular crystals using a ray-tracing approach
Diederichs, K. (2009) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909010282 · Cited by 24 · see citing works
Self-citationStructural Analysis of a Putative Aminoglycoside N-Acetyltransferase from Bacillus anthracis
Klimecka, M. M., Chruszcz, M., Font, J., et al. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.04.076 · Cited by 20 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
An oral SARS-CoV-2 M <sup>pro</sup> inhibitor clinical candidate for the treatment of COVID-19
Owen, D. R., Allerton, C. M. N., Anderson, A. S., Aschenbrenner, L., Avery, M., Berritt, S., Boras, B., Cardin, R. D., Carlo, A., Coffman, K. J., et al. (2021) · Science · doi:10.1126/science.abl4784 · Cited by 2,033 · see citing works
The target landscape of clinical kinase drugs
Klaeger, S., Heinzlmeir, S., Wilhelm, M., Polzer, H., Vick, B., Koenig, P.-A., Reinecke, M., Ruprecht, B., Petzoldt, S., Meng, C., et al. (2017) · Science · doi:10.1126/science.aan4368 · Cited by 854 · see citing works
Accurate assessment of mass, models and resolution by small-angle scattering
Rambo, R. P., & Tainer, J. A. (2013) · Nature · doi:10.1038/nature12070 · Cited by 750 · see citing works
Structural basis of lenalidomide-induced CK1α degradation by the CRL4CRBN ubiquitin ligase
Petzold, G., Fischer, E. S., & Thomä, N. H. (2016) · Nature · doi:10.1038/nature16979 · Cited by 620 · see citing works
Design of protein-binding proteins from the target structure alone
Cao, L., Coventry, B., Goreshnik, I., Huang, B., Sheffler, W., Park, J. S., Jude, K. M., Marković, I., Kadam, R. U., Verschueren, K. H. G., et al. (2022) · Nature · doi:10.1038/s41586-022-04654-9 · Cited by 577 · see citing works
Czabotar, P. E., Westphal, D., Dewson, G., Ma, S., Hockings, C., Fairlie, W. D., Lee, E. F., Yao, S., Robin, A. Y., Smith, B. J., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.031 · Cited by 573 · see citing works
The molecular basis of JAK/STAT inhibition by SOCS1
Liau, N. P. D., Laktyushin, A., Lucet, I. S., Murphy, J. M., Yao, S., Whitlock, E., Callaghan, K., Nicola, N. A., Kershaw, N. J., & Babon, J. J. (2018) · Nature Communications · doi:10.1038/s41467-018-04013-1 · Cited by 456 · see citing works
SARS-CoV-2 M <sup>pro</sup> inhibitors with antiviral activity in a transgenic mouse model
Qiao, J., Li, Y.-S., Zeng, R., Liu, F.-L., Luo, R.-H., Huang, C., Wang, Y.-F., Zhang, J., Quan, B., Shen, C., et al. (2021) · Science · doi:10.1126/science.abf1611 · Cited by 465 · see citing works
The role of protein dynamics in the evolution of new enzyme function
Campbell, E., Kaltenbach, M., Correy, G. J., Carr, P. D., Porebski, B. T., Livingstone, E. K., Afriat-Jurnou, L., Buckle, A. M., Weik, M., Hollfelder, F., et al. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2175 · Cited by 311 · see citing works
Kershaw, N. J., Murphy, J. M., Liau, N. P. D., Varghese, L. N., Laktyushin, A., Whitlock, E. L., Lucet, I. S., Nicola, N. A., & Babon, J. J. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2519 · Cited by 301 · see citing works
Transferrin receptor 1 is a reticulocyte-specific receptor for <i>Plasmodium vivax</i>
Gruszczyk, J., Kanjee, U., Chan, L.-J., Menant, S., Malleret, B., Lim, N. T. Y., Schmidt, C. Q., Mok, Y.-F., Lin, K.-M., Pearson, R. D., et al. (2018) · Science · doi:10.1126/science.aan1078 · Cited by 212 · see citing works
De novo protein design enables the precise induction of RSV-neutralizing antibodies
Sesterhenn, F., Yang, C., Bonet, J., Cramer, J. T., Wen, X., Wang, Y., Chiang, C.-I., Abriata, L. A., Kucharska, I., Castoro, G., et al. (2020) · Science · doi:10.1126/science.aay5051 · Cited by 191 · see citing works
The Yeast Ski Complex: Crystal Structure and RNA Channeling to the Exosome Complex
Halbach, F., Reichelt, P., Rode, M., & Conti, E. (2013) · Cell · doi:10.1016/j.cell.2013.07.017 · Cited by 210 · see citing works
Brouwer, J. M., Westphal, D., Dewson, G., Robin, A. Y., Uren, R. T., Bartolo, R., Thompson, G. V., Colman, P. M., Kluck, R. M., & Czabotar, P. E. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.07.016 · Cited by 161 · see citing works
Rosenberg, O. S., Dovala, D., Li, X., Connolly, L., Bendebury, A., Finer-Moore, J., Holton, J., Cheng, Y., Stroud, R. M., & Cox, J. S. (2015) · Cell · doi:10.1016/j.cell.2015.03.040 · Cited by 134 · see citing works
Structural determinants of integrin β-subunit specificity for latent TGF-β
Dong, X., Hudson, N. E., Lu, C., & Springer, T. A. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2905 · Cited by 141 · see citing works
Crystal structure of the Rous sarcoma virus intasome
Yin, Z., Shi, K., Banerjee, S., Pandey, K. K., Bera, S., Grandgenett, D. P., & Aihara, H. (2016) · Nature · doi:10.1038/nature16950 · Cited by 95 · see citing works
Olivier, N. B., Altman, R. B., Noeske, J., Basarab, G. S., Code, E., Ferguson, A. D., Gao, N., Huang, J., Juette, M. F., Livchak, S., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1414401111 · Cited by 48 · see citing works
Malmirchegini, G. R., Sjodt, M., Shnitkind, S., Sawaya, M. R., Rosinski, J., Newton, S. M., Klebba, P. E., & Clubb, R. T. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.583013 · Cited by 33 · see citing works
Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry
Nowak, E., Miller, J. T., Bona, M. K., Studnicka, J., Szczepanowski, R. H., Jurkowski, J., Le Grice, S. F. J., & Nowotny, M. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2785 · Cited by 31 · see citing works
- Authors
- Karplus, P. A., & Diederichs, K.
- Affiliations
- Oregon State University (US)
- University of Konstanz (DE)
- Corresponding author
- Diederichs, Kay
- Venue
- Science
- Published
- 2012-05-25
- Volume
- 336
- Issue
- 6084
- Pages
- 1030-1033
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3457925
- OpenAlex
- W2108959691
- Cited by
- 1,781
- References
- 27
- Citations by year
- 2026: 42 · 2025: 73 · 2024: 84 · 2023: 111 · 2022: 104 · 2021: 107 · 2020: 135 · 2019: 135 · 2018: 142 · 2017: 154 · 2016: 189 · 2015: 186 · 2014: 187 · 2013: 110 · 2012: 21
- FWCI
- 74.23
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- KOPS (University of Konstanz) (submittedVersion)
- DORA PSI (Paul Scherrer Institute) (submittedVersion)
- Funders
- Alexander von Humboldt-Stiftung
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM083136, GM083136)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK-056649, R01DK056649)
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Materials Science › Materials Chemistry › X-ray Diffraction in Crystallography
- Physical Sciences › Chemistry › Inorganic Chemistry › Crystal structures of chemical compounds
- Keywords
- protein crystallography, model-data agreement, data quality, statistical models, anomalous diffraction, phase problem, macromolecular structure
- MeSH terms
- Data Interpretation, Statistical, Models, Molecular, Protein Conformation, Proteins, Research Design, Crystallography, X-Ray, Cysteine Dioxygenase
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