Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit.

Fengyun Ni,Billy K Poon,Jianpeng Ma,Qinghua Wang

doi:10.1107/s0907444909010695

Abstract

The structural refinement of large complexes at the lower resolution limit is often difficult and inefficient owing to the limited number of reflections and the frequently high-level structural flexibility. A new normal-mode-based X-ray crystallographic refinement method has recently been developed that enables anisotropic B-factor refinement using a drastically smaller number of thermal parameters than even isotropic refinement. Here, the method has been systematically tested on a total of eight systems in the resolution range 3.0-3.9 A. This series of tests established the most applicable scenarios for the method, the detailed procedures for its application and the degree of structural improvement. The results demonstrated substantial model improvement at the lower resolution limit, especially in cases in which other methods such as the translation-libration-screw (TLS) model were not applicable owing to the poorly converged isotropic B-factor distribution. It is expected that this normal-mode-based method will be a useful tool for structural refinement, in particular at the lower resolution limit, in the field of X-ray crystallography.

Highlights

For structural refinement in X-ray crystallography, temperature B factors are used to account for structural deviations from the average positions of atoms
The large number of independent thermal parameters in the isotropic B-factor model, which is generally equal to the number of non-H atoms in the asymmetric unit, imposes a severe burden for lower resolution refinement owing to the low data-to-parameter ratio
The highly flexible components in large complexes very frequently compromise the resolution of diffraction, making a full-scale anisotropic refinement that requires six independent thermal parameters for each non-H atom in the asymmetric unit impossible

Summary

Introduction

For structural refinement in X-ray crystallography, temperature B factors are used to account for structural deviations from the average positions of atoms. The large number of independent thermal parameters in the isotropic B-factor model, which is generally equal to the number of non-H atoms in the asymmetric unit, imposes a severe burden for lower resolution refinement owing to the low data-to-parameter ratio (risk of overfitting). The independence of atomic thermal factors across proteins results in many cases in poor representation of collective molecular motions. This is a severe problem for large and flexible complex structures, the functions of which often involve long-range collective deformations. The highly flexible components in large complexes very frequently compromise the resolution of diffraction, making a full-scale anisotropic refinement that requires six independent thermal parameters for each non-H atom in the asymmetric unit impossible

Methods

Results

Conclusion