Table 2. Structure solution and refinement.
Values in parentheses are for the outer shell.
| Data set | Apo GPX4WT | GPX4C66S–(S)-ML162 |
|---|---|---|
| PDB code | 6hn3 | 6hkq |
| Resolution range (Å) | 33.97–1.01 (1.03–1.01) | 46.81–1.54 (1.58–1.54) |
| Completeness (%) | 94.7 | 86.6 |
| No. of reflections, working set | 71219 | 19002 |
| No. of reflections, test set | 3749 | 951 |
| Final R cryst | 0.115 (0.250) | 0.150 (0.226) |
| Final R free | 0.137 (0.265) | 0.184 (0.295) |
| No. of non-H atoms | ||
| Protein | 1470 | 1365 |
| Chloride ion/ethanol | 5 | n/a |
| ML162 | n/a | 32 |
| SO4 2− ion/ethylene glycol | n/a | 21 |
| Solvent | 248 | 228 |
| Total | 1723 | 1646 |
| R.m.s. deviations | ||
| Bonds (Å) | 0.016 | 0.013 |
| Angles (°) | 1.877 | 1.701 |
| Average B factors (Å2) | ||
| Protein | 13.8 | 17.2 |
| Chloride ion/ethanol | 18.4 | n/a |
| ML162 | n/a | 26.9 |
| SO4 2− ion/ethylene glycol/DMSO | n/a | 45.4 |
| Water | 27.0 | 30.6 |
| Ramachandran plot† | ||
| Most favored (%) | 98.6 | 98.7 |
| Allowed (%) | 1.4 | 1.3 |
| MolProbity score‡ | 1.72 | 1.09 |
†
Ramachandran statistics calculated with Coot.
‡
MolProbity score calculated using the server at http://molprobity.biochem.duke.edu/.