Checking for Gross Errors and Estimating the Accuracy of the Structural Model

Abstract

After the molecular model of the protein structure has been refined, it may still contain errors that have creeped into the model during the interpretation of the electron density map, particularly of the regions where the electron density is weak. Some of the errors are obvious and should cause immediate suspicion, for instance, the presence of left-handed helices can almost always be ruled out. Most of the available modeling programs allow regularization of geometry, but do not guarantee overall good quality of the final model. A very qualitative impression of the accuracy of the structural model can be obtained by inspection of the electron density map:

• the connectivity of the main chain and the side chains

• the bulging out of the carbonyl oxygen atoms from the main chain

• the interpretation of the side chain electron density.