TABLE 7.
Crystal data, data collection parameters and structure refinement statistics
| Complex | G:dCMPNPP (Cn) | 8-OxoG:dCMPNP (Ci) | 8-OxoG:dAMPNPP (Ai) | 8-OxoG:dGMPNPP (Gi) | 8-OxoG:C (Ce) | 8-OxoG:A (Ae) |
|---|---|---|---|---|---|---|
| Data collection | ||||||
| Wavelength Å | 1.07810 Å | 0.97872 Å | 1.07810 Å | 0.97872 Å | 0.97872 Å | 0.97872 Å |
| Space group | P61 | P61 | P61 | P61 | P61 | P61 |
| Resolution | 42.24 to 1.58 Å (1.64 to 1.58 Å)a | 42.52 to 1.72 Å (1.78 to 1.72 Å) | 42.68 to 1.70 Å (1.76 to 1.70 Å) | 42.59 to 1.72 Å (1.78 to 1.72 Å) | 42.57 to 1.72 Å (1.78 to 1.72 Å) | 42.70 to 1.62 Å (1.68 to 1.62 Å) |
| Unit cell a = b, c | 98.66, 81.79 Å | 98.20, 81.55 Å | 98.57, 81.56 Å | 98.37, 81.70 Å | 98.31, 81.60 Å | 98.61, 81.84 Å |
| Unique reflections | 61,923 (6,148) | 47,424 (4,714) | 49,367 (4,854) | 47,675 (4,752) | 47,720 (4,725) | 57,391 (5,696) |
| Completeness [%] | 99.9 (99.7) | 99.9 (99.7) | 99.5 (98.6) | 99.9 (99.9) | 99.7 (99.0) | 100.0 (100.0) |
| I/σ(I) | 20.86 (2.33) | 23.73 (4.29) | 15.65 (1.92) | 18.35 (2.93) | 26.32 (3.94) | 15.33 (3.21) |
| Wilson B-factor | 19.4 Å2 | 19.1 Å2 | 23.7 Å2 | 21.0 Å2 | 21.1 Å2 | 17.1 Å2 |
| R-merge | 0.065 (0.863) | 0.070 (0.647) | 0.064 (0.948) | 0.082 (0.827) | 0.065 (0.755) | 0.099 (0.806) |
| Redundancy | 7.4 (7.2) | 7.3 (6.7) | 7.4 (6.9) | 7.5 (7.4) | 7.2 (6.6) | 7.4 (6.5) |
| Refinement | ||||||
| R-work | 0.170 (0.233) | 0.163 (0.211) | 0.172 (0.244) | 0.185 (0.271) | 0.172 (0.228) | 0.162 (0.199) |
| R-free | 0.215 (0.269) | 0.208 (0.253) | 0.219 (0.294) | 0.232 (0.351) | 0.210 (0.270) | 0.204 (0.238) |
| No. of atoms protein/DNA | 3,459/409 | 3,470/410 | 3,441/410 | 3,517/430 | 3,380/409 | 3,445/413 |
| dNMPNPP/Mg2+ | 28/2 | 28/2 | 30/2 | 31/2 | 28/2 | 28/2 |
| Water/solute | 475/6 | 466/12 | 424/6 | 462/6 | 452/6 | 532/12 |
| Protein residues | 450 | 451 | 451 | 450 | 447 | 449 |
| Average B-factor | 26.0 | 24.4 | 30.7 | 26.6 | 28.6 | 24.4 |
| Protein/DNA | 24.9/27.3 | 23.1/26.8 | 29.7/31.5 | 25.2/31.3 | 27.4/31.4 | 23.1/26.4 |
| dNMPNPP/Mg2+ | 15.2/13.6 | 12.1/10.6 | 18.8/13.5 | 16.7/14.8 | 16.4/17.8 | 13.0/19.6 |
| Water/solute | 33.0/16.7 | 32.7/21.7 | 38.0/23.1 | 34.3/18.1 | 36.2/17.9 | 31.7/22.4 |
| r.m.s.b (bonds) | 0.019 | 0.015 | 0.017 | 0.014 | 0.012 | 0.015 |
| r.m.s. (angles) | 1.8 | 1.4 | 1.5 | 1.2 | 1.2 | 1.4 |
| Ramachandran, favored | 98% | 98% | 97% | 97% | 98% | 98% |
| Ramachandran, outliers | 0.23% | 0.23% | 0.46% | 0.22% | 0.47% | 0.46% |
a Statistics for the highest resolution shell are shown in parentheses.
b r.m.s. is root mean square.