DETERMINATION OF THE RELATIVE PRECISION OF ATOMS IN A MACROMOLECULAR STRUCTURE

Several real-space indices and temperature factors are compared with r espect to their correlation with atomic positional error and their abi lity to indicate atoms and residues with the worst of subtle errors. T he best index, r(ED) is a correlation coefficient between model and ma p electron densities, similar to one proposed earlier, but incorporati ng two improvements. Firstly, resolution is accounted for explicitly b y calculating the model electron density by Fourier transformation of resolution-truncated scattering factors. Secondly, the deviation betwe en model and map electron densities is assigned to neighboring atoms a ccording to their contribution to the electron density of each grid po int. With maps of various qualities, r(ED) is the single index with be st correlation to atomic error with grouped or individual atoms, and i t is the most reliable indicator of poor residues. With poorer omit ma ps, imprecision of individual atoms is best diagnosed by a combination of low r(ED) or high B factor. With the improved methods, 60-70% of t he least precise atoms can detected in a fully refined structure. Simi larly, 40-80% of the least precise atoms of an unrefined modal can be detected by comparison with an isomorphous replacement map. This is us eful in assessing and improving the quality of a model, but not suffic ient to confidently validate all atoms of a structure at sub-atomic re solution.