Electron density map evaluation functions for determining the quality of protein crystal structures

Abstract

Background

Finding methods to judge the quality of X-ray crystallographic information is an active research topic. The quality of electron density maps reconstructed by Fourier transform is always limited by the finite resolution, the amplitude/phase error and the completeness of diffraction data. At present, the R value and effective resolution are common ways of evaluating the quality of electron density maps. Unfortunately, the current evaluation methods are only dependent on diffraction amplitude, without any phase information.

Methods

Advanced evaluation functions in real space are designed to estimate the electron density map quality. The electron density map definition evaluation function relies on the atomicity of the electron density distribution. We use the power spectrum electron density entropy in protein crystallography for the first time. These two functions include both structure factor amplitudes and phases via the Fourier transform of electron density map.

Results

We carry out tests on synthetic data sets of known structures, varying the resolution and error, and draw the quality curves of electron density maps with theoretical, noisy and experimental diffraction data by two evaluation functions at different resolutions. The curves reveal the optimum structure and resolution of proteins clearly.

Conclusions

The work presented here offers new methods to evaluate the qualities of the electron density maps of proteins with slight differences, and brand new indicators to select the optimum diffraction resolution of protein structures.