Coot

[…] ined with PHENIX Phaser software using molecular replacement function and a polyalanine scaffold of TacT (PDB 5FVJ) as a model. The model was then modified using AutoBuild and manually improved using Coot and refined using PHENIX and Refmac, against the high-resolution native data to give a final structure with an Rfree of 23.1% and good geometry (Supplementary Table ). The relatively high final […]

[…] ssion: 1A0R, 5M2W) with the CCP4 program PHASER,. Initial models were improved by multiple rounds of REFMAC ver. 5.8 refinement against the Gβ1γ1-Nb5 complex dataset and manual model adjustments with Coot 0.8.8. The final models had agreement factors Rfree and Rcryst of 24.7% and 20%, respectively. The stereochemical quality of the Gβ1γ1-Nb5 complex model was assessed with the Molprobity and wwPDB […]

[…] chrotron (MX2) and processed using XDS. The structure was solved by molecular replacement with PHASER using the structure of NaD1 in its dimeric form as a search model. The final model was built with Coot and refined with Phenix to a resolution of 2.5 Å with the final Rwork and Rfree values of 0.2031 and 0.2519, respectively. All data collection and refinement statistics are summarized in Table . […]

[…] +PGT122 complex structure was determined by MR with PGV19 (determined in this study) and BG505 SOSIP.664+PGT122 from PDB 4TVP. The structures were refined using Phenix and model building performed in Coot. MolProbity, Privateer, and pdb-care were used for structure validation. The refinement statistics are reported in Supplementary Table . […]

[…] tructions. The non-hydrogen atoms were analyzed anisotropically, and hydrogen atoms were input at the calculated positions and refined with a riding model. Electron density mapping was performed on a COOT software program. The Hirshfeld surface analyses were performed using the CrystalExplorer software program. The refinement data are shown in Supplementary Tables –. […]

[…] e molecular replacement program Phaser using a previously reported complex structure of rat DPP-IV with Fab 11A19 (PDB code: 4FFV) as a search model. Model building and refinement were carried out in COOT and REFMAC in CCP4, respectively. All structural figures were prepared using PyMOL (Schrodinger Inc, San Diego, CA). […]