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 might still contain errors that have creeped into the model during the interpretation of the electron density map, particularly in 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: