Open AccessImproved crystallographic models through iterated local density‐guided model deformation and reciprocal‐space refinement
Author(s) -
Terwilliger Thomas C.,
Read Randy J.,
Adams Paul D.,
Brunger Axel T.,
Afonine Pavel V.,
GrosseKunstleve Ralf W.,
Hung LiWei
Publication year - 2012
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444912015636
Subject(s) - iterated function , algorithm , reciprocal lattice , computer science , molecular replacement , process (computing) , geometry , convergence (economics) , reciprocal , topology (electrical circuits) , mathematics , crystallography , physics , crystal structure , mathematical analysis , combinatorics , chemistry , linguistics , philosophy , diffraction , optics , economics , economic growth , operating system
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.