TABLE 3.
Crystal data, data collection parameters, and structure refinement statistics
| Complex | O6-MeG:dCTP insertion | O6-MeG:dTMP -NPP insertion | O6-MeG:dC extension | O6-MeG:dT extension |
|---|---|---|---|---|
| Data Collection | ||||
| Wavelength (Å) | 0.97856 | 1.07810 | 0.97872 | 0.97872 |
| Space group | P61 | P61 | P61 | P61 |
| Resolution (Å) | 50-2.79 (2.79-2.84)a | 50-1.94 (1.94-1.97) | 50-1.82 (1.82-1.85) | 50-1.62 (1.62-1.65) |
| Unit cell a = b, c (Å) | 99.09, 81.89 | 99.00, 81.70 | 98.46, 82.11 | 98.36, 82.03 |
| Unique reflections | 11,577 (581) | 33,771 (1,684) | 40,671 (2,018) | 57,284 (2,831) |
| Completeness (%) | 99.9 (99.8) | 100 (100) | 100 (100) | 100 (100) |
| I/σ(I) | 10.65 (1.58) | 27.38 (1.78) | 14.55 (1.85) | 23.18 (2.04) |
| Wilson B-factor (Å2) | 35.0 | 27.0 | 15.4 | 15.5 |
| R-merge | 0.169 (0.966) | 0.091 (0.819) | 0.118 (0.809) | 0.098 (0.869) |
| Redundancy | 5.5 (5.2) | 7.6 (7.5) | 5.7 (5.6) | 7.6 (7.2) |
| Refinement | ||||
| R-work | 0.159 (0.226) | 0.159 (0.183) | 0.153 (0.203) | 0.156 (0.187) |
| R-free | 0.228 (0.266) | 0.201 (0.281) | 0.187 (0.232) | 0.193 (0.240) |
| Number of atoms protein/DNA | 3,372/409 | 3,450/395 | 3,412/390 | 3,433/391 |
| dNMP-NPP/Mg2+ | 28/2 (Ca2+) | 29/2 | 28/2 | 28/2 |
| Water/solute | 138/2 | 410/1 | 491/1 | 526/3 |
| Protein residues | 430 | 430 | 430 | 430 |
| B-factor (Å2) | ||||
| Average | 49.1 | 33.6 | 23.8 | 24.4 |
| Protein/DNA | 49.4/55.5 | 33.1/37.3 | 22.9/30.9 | 23.1/33.3 |
| dNMP-NPP/Mg2+ | 30.5/38.9 | 30.3/26.8 | 11.2/8.5 | 13.3/10.9 |
| Water/ glycerol | 37.2/50.7 | 41.1/25.9 | 32.0/15.0 | 34.6/ 33.3 |
| Root mean square deviations | ||||
| Bonds (Å) | 0.010 | 0.018 | 0.018 | 0.017 |
| Angles (degress) | 1.5 | 1.8 | 1.8 | 1.8 |
| Ramachandran | ||||
| Favored (%) | 95 | 97 | 97 | 98 |
| Allowed (%) | 4.8 | 2.5 | 2.8 | 1.8 |
| Outliers (%) | 0.2 | 0.5 | 0.2 | 0.2 |
| PDB ID code | 5L1I | 5L1J | 5L1K | 5L1L |
a Statistics for the highest resolution shell are shown in parentheses.