Determination of the relative precision of atoms in a macromolecular structure

Several real-space indices and temperature factors are compared with respect to their correlation with atomic positional error and their ability to indicate atoms and residues with the worst of subtle errors. The best index, rED, is a correlation coefficient between model and map electron densities, similar to one proposed earlier, but incorporating two improvements. Firstly, resolution is accounted for explicitly by calculating the model electron density by Fourier transformation of resolution-truncated scattering factors. Secondly, the deviation between model and map electron densities is assigned to neighboring atoms according to their contribution to the electron density of each grid point. With maps of various qualities, rED is the single index with best correlation to atomic error with grouped or individual atoms, and it is the most reliable indicator of poor residues. With poorer omit maps, imprecision of individual atoms is best diagnosed by a combination of low rED or high B factor. With the improved methods, 60-70% of the least precise atoms can detected in a fully refined structure. Similarly, 40-80% of the least precise atoms of an unrefined model can be detected by comparison with an isomorphous replacement map. This is useful in assessing and improving the quality of a model, but not sufficient to confidently validate all atoms of a structure at sub-atomic resolution.