Residues were mutated from the PtGPX5 sequence to that of TbTDPX2 using COOT [ 19], and further cycles of restrained refinement interspersed with electron-density inspection, manual model building and manipulation and water addition were performed with REFMAC5 and COOT.
Phasing, automated and manual model building, and refinement produced an atomic model of very good quality, resolving residues 1 168 of ZapC, with two molecules in the asymmetric unit, at 2.9 Å resolution (Table 1).
Coot (Emsley and Cowtan, 2004) was used for manual model building, and Refmac (Murshudov et al, 1997) and Phenix (Zwart et al, 2008) for structure refinement.
Manual model building and refinement were performed using COOT (Emsley and Cowtan, 2004) and PHENIX (Adams et al., 2010).
Manual model building and refinement were performed using COOT (Emsley and Cowtan, 2004) and PHENIX (Adams et al., 2010) following rigid body refinement, energy minimization, B-factor refinement, and group NCS constraints.
COOT [ 31] was used for manual model building and refinement, whereas REFMAC [ 32] and PHENIX.REFINE [ 33] were used for automated refinement.
Manual model improvements and refinement were carried out in COOT[32] and REFMAC[33], respectively.
Iterative runs of ARP/wARP combined with manual model building and iterative cycles of refinement in REFMAC were used to complete and refine the model at 1.55 Å resolution.
Once manual model building and refinement converged43, the TLS option44, 45 was introduced in REFMAC.
After several cycles of manual model building and structural refinement, the electron density corresponding to the inhibitor was clearly observed.
