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

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.

Figure 1

Application of morphing to the cab55348 structure. (a) Cip2 template (Pokkuluri et al., 2011 ▶) in blue; final model of cab55348 in green; prime-and-switch electron-density map based on the template structure in purple. (b) Cip2 template and map as in (a); template after refinement with phenix.refine in orange. (c) Cip2 template and map as in (a); model density calculated from Cip2 template in purple. (d) Cip2 map as in (a); model density calculated from Cip2 template, offset to optimally match map, in purple. (e) Cip2 template and map as in (a); morphed Cip2 model in yellow. (f) Cip2 template, map and morphed Cip2 model as in (e); refined morphed Cip2 model in off-yellow. (g) Refined model after six cycles of morphing in yellow; prime-and-switch map based on model from cycle 5 of morphing in purple. (h) Automatically rebuilt model in green and density-modified electron density map in blue obtained starting from the map and model in (g). Contour levels in all the maps are at 1.5σ except for the model densities in (c) and (d), which are at 3.5σ. Figures were created with Coot (Emsley et al., 2010 ▶) and Raster3D (Merritt & Bacon, 1997 ▶). A full Coot scene with all models and maps is available as supplementary material.

Figure 2

Differences between templates, refined and morphed models and the best available models for each structure. For each structure (listed along the x axis), the r.m.s.d. or percentile-based spread between the best available model for that structure and (i) the template, (ii) the template after three cycles of refinement with phenix.refine, (iii) the template after 100 cycles of refinement and (iv) the template after morphing using the prime-and-switch maps and iterating the morphing process for a total of 12 cycles is shown. (a) Differences calculated as r.m.s.d. (b) Differences calculated as percentile-based spread.