Q - score as a reliability measure for protein, nucleic acid, and small molecule atomic coordinate models derived from 3DEM density maps

Abstract

Atomic coordinate models are important in the interpretation of 3D maps produced with cryoEM and sub-tomogram averaging in cryoET, or more generically, 3D electron microscopy (3DEM). In addition to visual inspection of such maps and models, quantitative metrics convey the reliability of the atomic coordinates, in particular how well the model is supported by the experimentally determined 3DEM map. A recently introduced metric, $Q\text{-}\mathrm{score}$ , was shown to correlate well with the reported resolution of the map for well-fitted models. Here we present new statistical analyses of $Q\text{-}\mathrm{scores}$ based on its application to $\sim$ 10,000 maps and models archived in EMDB and PDB. Further we introduce two new metrics based on $Q\text{-}\mathrm{score}$ : $Q\text{-}\mathrm{relative}\text{-}\mathrm{all}$ and $Q\text{-}\mathrm{relative}\text{-}\mathrm{resolution}$ to compare a map and model to all entries in the EMDB and those with similar resolution respectively. We also explore through illustrative examples of proteins, nucleic acids, and small molecules how $Q\text{-}\mathrm{scores}$ can indicate whether the atomic coordinates are well-fitted to 3DEM maps and whether some parts of a map may be poorly resolved due to factors such as molecular flexibility, radiation damage, and/or conformational heterogeneity. Lastly, we show examples of how $Q\text{-}\mathrm{scores}$ can effectively be converted to atomic $B\text{-}\mathrm{factors}$ . These analyses provide a basis for how $Q\text{-}\mathrm{scores}$ can be interpreted effectively to evaluate 3DEM maps and atomic coordinate models prior to publication and archiving.

Keywords: B-factors; CryoEM; Q scores; structure; validation.