Shift-field refinement of macromolecular atomic models.

K Cowtan,S Metcalfe,P Bond

doi:10.1107/s2059798320013170

Abstract

The aim of crystallographic structure solution is typically to determine an atomic model which accurately accounts for an observed diffraction pattern. A key step in this process is the refinement of the parameters of an initial model, which is most often determined by molecular replacement using another structure which is broadly similar to the structure of interest. In macromolecular crystallography, the resolution of the data is typically insufficient to determine the positional anduncertainty parameters for each individual atom, and so stereochemical information is used to supplement the observational data. Here, a new approach to refinement is evaluated in which a `shift field' is determined which describes changes to model parameters affecting whole regions of the model rather than individual atoms only, with the size of the affected region being a key parameter of the calculation which can be changed in accordance with the resolution of thedata. It is demonstrated that this approach can improve the radius of convergence of the refinement calculation while also dramatically reducing the calculation time.

Highlights

Crystallographic refinement, in which the parameters of an atomic model are optimized to best explain an observed diffraction pattern, is an important stage in the structuresolution process
There are a subset of cases where the reduction in free R factor is far more substantial, with the extreme case being PDB entry 4c2q, where the inclusion of jelly-body refinement leads to a reduction in the free R factor of 15%
We have shown that shift-field refinement can complement conventional model-refinement methods in two major ways: firstly, the calculation can be conducted at low resolution, with benefits in terms of both speed and radius of convergence; secondly, the calculation is very fast, usually converging in fewer cycles than conventional or jelly-body refinement

Summary

Introduction

Crystallographic refinement, in which the parameters of an atomic model are optimized to best explain an observed diffraction pattern, is an important stage in the structuresolution process. Crystallographic refinement has traditionally involved the optimization of positional, thermal and other parameters that describe each individual atom in the crystal structure (Driessen et al, 1989). In the case of macromolecular refinement, disorder and thermal motion limit the resolution of the diffraction pattern and the number of available observations; this means that the data are insufficient to allow us to uniquely determine all of the atomic parameters. The diffraction observations and stereochemical restraints introduce very different patterns of correlation among model parameters: each diffraction observation impacts every positional coordinate, whereas any given geometric restraint affects only a small number of atoms, introducing strong correlations between the coordinate parameters of those atoms. The use of stereochemical restraints leads to a substantial increase in the complexity of

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Conclusion