The<i>PDB_REDO</i>server for macromolecular structure model optimization

“…Structure refinement was carried out using REFMAC5 (52), interspersed with manual rebuilding using COOT (53). In the penultimate round, the models were optimized using the PDB_REDO server (54). In the final round, each module (GH5, Ig_Like and CBM46) was treated as a single group for anisotropic TLS refinement.…”

“…Phases were obtained using autoSHARP, which located one selenomethionine (43). The structure was built, refined, and validated using autoSHARP, Coot, Refmac, and the PDB_REDO server (43)(44)(45)(46)(47). The figures were made using the UCSF Chimera package (48).…”

“…20 The structure was refined with multiple rounds of simulated annealing and composite omit maps (no crystallographic symmetry averaging) using the program Phenix 42 followed by rounds of model building using Coot. 44 PDB_REDO 43 was used for refinement validation. The model refinement converged at an R work D 22 .1% and R free D 24 .9%.…”