Systematic analysis of residual density suggests that a major limitation in well-refined X-ray structures of proteins is the omission of ordered solvent.

ABSTRACT: In the residual electron density map of a fully refined X-ray protein model, there should be no peaks arising from modeling errors or missing atoms. Any residual peaks that do occur should be contributed by random residual intensity differences between the model and the data. If the model is incomplete (i.e., some atoms are missing), there will be more positive peaks than negative ones. On the other hand, if the model includes inappropriately located atoms, there will be an excess of negative peaks. In this study, random residual peaks are quantified using the probability density function P(x), which is defined as the probability for a peak having peak height between x and x + dx. It is found that P(x) is single-exponential and symmetric for both positive and negative peaks. Thus, P(x) can

SUBMITTER: Wang J 

PROVIDER: S-EPMC5405434 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature