Measurement of atom resolvability in cryo-EM maps with Q-scores.

Abstract

CryoEM density 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 cryoEM 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 cryoEM 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 cryoEM maps for both protein and RNA. Assuming the models they are calculated from are well-fitted to the map, Q-scores can thus be used as a measure of resolvability in cryoEM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryoEM maps of the same proteins derived from different labs confirms the reproducibility of structural features from side chains down to water and ion atoms.