Measurement of Atom Resolvability in CryoEM Maps with Q-scores
By Grigore D. Pintilie, Kaiming Zhang, Z. Su, Shanshan Li, M. Schmid, Wah Chiu. 2019
272 citations recorded by the source corpus.
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.
Subfields: Condensed Matter Physics, Molecular Biology, Structural Biology
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In Molecular Biology
- R. Rangan
- Eric Westhof
- Rhiju Das
- Zhichao Miao
- Thomas Mulvaney
- Daniel J. Rigden
- J. Beton
- Phillip Pham
In Structural Biology
Citations in the corpus
- Assessment of three-dimensional RNA structure prediction in CASP15 (2023, positive): “The following programs were used to measure the listed metrics, in all cases using default parameters (1) Phenix, 37 43 and density occupancy; and (4) MapQ, 44 for Q-score.”
- Integrating model simulation tools and cryo‐electron microscopy (2022, methodology): “The inverse was true for the cluster of scoring functions that included EMRinger, Q-score, and FSC05, all of which give higher scores on average as the map resolution improves.”