Table 1. X-ray crystallographic data and final protein plus ligand model-refinement statistics for both the cisplatin and carboplatin crystals.
Cisplatin/NaI | Carboplatin/NaI | |
---|---|---|
PDB code | 4ow9 | 4owa |
Data-collection temperature (K) | 100 | 100 |
Data reduction | ||
Space group | P21 | P21 |
Unit-cell parameters (Å, °) | a = 27.25, b = 62.54, c = 58.98, β = 90.92 | a = 27.14, b = 62.28, c = 58.05, β = 92.59 |
Molecules per asymmetric unit | 2 | 2 |
Observed reflections | 110261 | 104255 |
Unique reflections | 11636 | 20257 |
Resolution (Å) | 31.27–2.10 (2.15–2.10) | 29.04–1.80 (1.90–1.80) |
Completeness (%) | 90.1 (55.7) | 94.3 (78.0) |
R merge (%) | 0.130 (0.229) | 0.099 (0.340) |
〈I/σ(I)〉 | 11.7 (3.5) | 11.7 (1.9) |
Multiplicity | 6.9 (1.6) | 5.7 (1.4) |
Refinement | ||
Cruickshank DPI (Å) | 0.11 | 0.18 |
No. of atoms | ||
Protein | 2002 | 2002 |
Water molecules | 39 | 147 |
Pt and halogen atoms | 34 | 42 |
Other bound atoms | 28 | 28 |
Average B factor (Å2) | ||
Protein atoms | 21.1 | 12.2 |
Water molecules | 18.8 | 19.2 |
Pt and halogen atoms | 29.1 | 20.9 |
Other bound atoms | 24.8 | 18.4 |
R factor/R free (%) | 19.7/27.1† | 18.4/24.0 |
R.m.s.d., bonds (Å)/angles (°) | 0.010/1.5 | 0.015/1.6 |
Ramachandran values (%) | ||
Most favoured | 94.1 | 96.5 |
Additional allowed | 5.2 | 3.1 |
Disallowed | 0.8‡ | 0.4‡ |
The PDB validation report includes phenix.xtriage statistics; subsequent use of DETWIN in CCP4 suggested that the data were 6% twinned. To our knowledge, no twinning has been reported for this form of HEWL in NaI conditions before. Turning on amplitude twin refinement in REFMAC improved the R/R free from 19.7/27.5% to 19.7/27.1%. The electron-density maps at the His binding sites as well as in general were the same with and without using twin refinement, presumably owing to the rather small twin fraction.
The disallowed residues are Asp18, Ser72 and Arg73 and are part of a loop/turn region.