Difference density quality (DDQ): a method to assess the global and local correctness of macromolecular crystal structures

Methods for the evaluation of the accuracy of crystal structures of protein s and nucleic acids are of general importance for structure-function studie s as well as for biotechnological and biomedical research based upon three- dimensional structures of biomacromolecules. The structure-validation progr am DDQ (difference-density quality) has been developed to complement existi ng validation procedures. The DDQ method is based on the information presen t in a difference electron-density map calculated with the water molecules deliberately omitted from the structure-factor calculation. The quality of a crystal structure is reflected in this difference map by (i) the height o f solvent peaks occurring at physical chemically reasonable positions with respect to protein and ligand atoms and (ii) the number and height of posit ive and negative 'shift' peaks next to protein atoms, The higher the solven t peaks and the lower the shift peaks, the better the structure is likely t o be. Moreover, extraneous positive density due to an incomplete molecular model is also monitored, since this is another indicator of imperfections i n the structure. Automated analysis of these types of features in differenc e electron densities is used to quantify the local as well as global accura cy of a structure. In the case of proteins, the DDQ structure-validation me thod is found to be very sensitive to small local errors, to omitted atoms and also to global errors in crystal structure determinations.