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TcdB was built using the published 3.87 Angstrom crystal structure as a starting model (PDB: 6OQ5). The three bound VHH domains in the crystal structu ...
TcdB was built using the published 3.87 Angstrom crystal structure as a starting model (PDB: 6OQ5). The three bound VHH domains in the crystal structure were removed in PyMOL, and the structure was docked into density using Chimera. The initial model was refined in Coot before alignment with the design model in PyMOL, the scFv docked well in density. The entire model was refined with iterative rounds in Coot, Interactive Structure Optimization by Local Direct Exploration (ISOLDE) were performed at a simulated 25 Kelvin, and Phenix real-space refinement. The final model quality was analyzed using Molprobity.