Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement.

Thomas C Terwilliger,Ralf W Grosse-Kunstleve,Paul D Adams,Randy J Read,Pavel V Afonine,Li-Wei Hung,Axel T Brunger

doi:10.1107/s0907444912015636

Abstract

An approach is presented for addressing the challenge of model rebuilding after molecular replacement in cases where the placed template is very different from the structure to be determined. The approach takes advantage of the observation that a template and target structure may have local structures that can be superimposed much more closely than can their complete structures. A density-guided procedure for deformation of a properly placed template is introduced. A shift in the coordinates of each residue in the structure is calculated based on optimizing the match of model density within a 6 Å radius of the center of that residue with a prime-and-switch electron-density map. The shifts are smoothed and applied to the atoms in each residue, leading to local deformation of the template that improves the match of map and model. The model is then refined to improve the geometry and the fit of model to the structure-factor data. A new map is then calculated and the process is repeated until convergence. The procedure can extend the routine applicability of automated molecular replacement, model building and refinement to search models with over 2 Å r.m.s.d. representing 65-100% of the structure.

Highlights

One of the most important methods for determining macromolecular structures is molecular replacement (Rossmann, 1972)
The starting model was the structure of the glucuronoyl esterase Cip2 (PDB entry 3pic; Pokkuluri et al, 2011), which was placed in the crystallographic unit cell of the target structure with Phaser (McCoy et al, 2007) with non-matching segments deleted and non-identical side chains trimmed beyond their C atoms, yielding a template containing 354 residues and having a sequence identity to the target of 32%
We find that morphing is quite powerful for improving the quality of models that principally differ from a target structure by simple deformations

Summary

Introduction

One of the most important methods for determining macromolecular structures is molecular replacement (Rossmann, 1972). These two structures must agree within about 1.5–2 Aroot-mean-square distance (r.m.s.d.) for C atoms over much of the molecules to be useful in molecular replacement (Chen et al, 2000) This means that the sequences of the template and target usually need to be about 25–30% identical or greater (Chothia & Lesk, 1986). Despite this limitation, over 70% of new protein structures are already determined by molecular replacement (Evans & McCoy, 2008). As the number and diversity of structures in the Protein Data Bank (PDB; Berman et al, 2000) increases, the applicability of molecular replacement will continue to broaden

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Conclusion