| simulated annealing | GB3 solution structure is obtained by refinement of the x-ray structure of gb3 (1igd) with c(alpha)-c', c'-n, c(alpha)-h(alpha) and N-H dipolar couplings measured in five aligning media (bicelle, peg, pf1 phage, negatively and positively charged polyacrylamide gels). Dipolar couplings originating on residues 10-11, 24-26, 39-41 and the n- and c-terminal residues were excluded, resulting in near-identity with the x-ray structure for these residues. This deposition corresponds to the refined-II structure of the primary citation that was refined against all 4 types of dipolar couplings in 5 media. The related depositions 1P7E and 1P7F correspond to the refined-III and refined-IV structures, respectively. The deposited structure was calculated with DYNAMO 2.1 following a short low-temperature molecular dynamics simulated annealing run starting from the regularized coordinates of the X-ray structure 1IGD using atomic coordinate restraints to the overlapping 3-residue segments of 1IGD. The force constants for the HN-N-C-Ca impropers were softened 10-fold relative to their standard settings. See the primary citation and the corresponding supporting information file for a detailed description of the refinement procedure. The deposited restraints file includes, in addition to the dipolar couplings and backbone H-bond distance restraints (XPLOR/CNS format), an Xplor-NIH script designed to mimic the deposited structure, and the force field parameter files. A set of overlapping 3-residue NCS restraint terms is used in this script in place of the Dynamo atomic coordinate restraints. | DYNAMO |
