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Measurement of atom resolvability in cryo-EM maps with Q-scores
Open accessAbstract
Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q -score. Q -scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q -scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q -scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Assuming the models they are calculated from are well fitted to the map, Q -scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q -score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms. Q -scores provide a quantitative metric for resolvability in cryo-EM maps, and can be used at the atom, residue or macromolecule scale.
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Cites
Coot : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571
PHENIX : 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
MolProbity : all-atom structure validation for macromolecular crystallography
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909042073 · Cited by 14,115
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Passos, D. O., Li, M., Jóźwik, I. K., Zhao, X. Z., Santos-Martins, D., Yang, R., Smith, S. J., Jeon, Y., Forli, S., Hughes, S. H., et al. (2020) · Science · doi:10.1126/science.aay8015 · Cited by 106
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Fadini, A., Li, M., McCoy, A. J., Banjara, S., Okumura, H., Napier, E., Fontana, P., Khan, A. R., Jovine, L., Terwilliger, T. C., et al. (2026) · Nature Methods · doi:10.1038/s41592-026-03047-4 · Cited by 22
Pintilie, G., Shao, C., Wang, Z., Hudson, B. P., Flatt, J. W., Schmid, M. F., Morris, K. L., Burley, S. K., & Chiu, W. (2025) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798325005923 · Cited by 21
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Chen, M. (2025) · Communications Biology · doi:10.1038/s42003-025-08202-9 · Cited by 11
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Marini, G., Poland, B., Leininger, C., Lukoyanova, N., Spielbauer, D., Barry, J. K., Altier, D., Lum, A., Scolaro, E., Ortega, C. P., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39891-7 · Cited by 9
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Connecting the dots: deep learning-based automated model building methods in cryo-EM
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Fonseca, N., Duraisamy, A. K., Wang, Z., Somasundharam, S., Tayebinia, M., de Oliveira, L. C., Ma, M., Turner, J., Patwardhan, A., Kleywegt, G. J., et al. (2026) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2026.1763403
Metadata
- Authors
- Pintilie, G., Zhang, K., Su, Z., Li, S., Schmid, M. F., & Chiu, W.
- Venue
- Nature Methods
- Published
- 2020-02-10
- Volume
- 17
- Issue
- 3
- Pages
- 328-334
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W3005016287
- Cited by
- 400
- References
- 3
- FWCI
- 17.49
- Type
- journal article
- Language
- en
- Open access
- green
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