TABLE 7.
Crystal data, data collection parameters, and structure refinement statistics
| Complex | ϵdA·dTTP | ϵdA·dAMPNPP | ϵdA·dGMPNPP | ϵdA·dT extension | ϵdA·dA extension |
|---|---|---|---|---|---|
| Data collection | |||||
| Wavelength (Å) | 0.97856 | 0.97872 | 0.97872 | 0.97856 | 0.97856 |
| Space group | P61 | P61 | P61 | P61 | P61 |
| Resolution (Å) | 50–2.26 (2.30–2.26)a | 50–2.12 (2.16–2.12) | 50–2.15 (2.19–2.15) | 50–2.30 (2.34–2.30) | 50–1.79 (1.82–1.79) |
| Unit cell a = b, c (Å) | 99.04, 81.83 | 99.13, 81.40 | 98.93, 81.71 | 98.42, 81.97 | 98.66, 82.00 |
| Unique reflections | 21,572 (1,058) | 25,919 (1,305) | 24,805 (1,213) | 20,156 (1,004) | 42,790 (2,112) |
| Completeness (%) | 100 (99.8) | 100 (100) | 100 (100) | 99.9 (99.9) | 99.7 (99.8) |
| I/σ(I) | 12.57 (1.70) | 15.90 (1.81) | 15.00 (1.70) | 11.80 (1.96) | 19.52 (1.83) |
| Wilson B-factor (Å2) | 18.5 | 26.7 | 25.7 | 15.1 | 17.6 |
| R-merge | 0.165 (0.893) | 0.135 (0.921) | 0.136 (0.996) | 0.169 (0.879) | 0.102 (0.902) |
| Redundancy | 7.3 (5.1) | 7.6 (7.2) | 7.6 (7.4) | 5.6 (5.1) | 7.5 (7.3) |
| Refinement | |||||
| R-work | 0.156 (0.196) | 0.175 (0.200) | 0.170 (0.221) | 0.156 (0.197) | 0.164 (0.204) |
| R-free | 0.212 (0.285) | 0.239 (0.271) | 0.223 (0.296) | 0.233 (0.295) | 0.212 (0.260) |
| No. of atoms protein/DNA | 3,387/390 | 3,395/390 | 3,397/390 | 3,367/374 | 3,429/374 |
| dNMPNPP/Mg2+ | 29/2 (Ca2+) | 30/2 | 31/2 | 29/2 | 29/2 |
| Water/solute | 351/1 | 308/3 | 343/1 | 332/0 | 532/2 |
| Protein residues | 434 | 436 | 436 | 431 | 447 |
| B-factor (Å2) | |||||
| Average | 29.7 | 35.1 | 33.9 | 27.4 | 23.7 |
| Protein/DNA | 28.9/33.4 | 34.3/37.7 | 32.9/38.5 | 26.3/33.9 | 21.7/28.5 |
| dNMPNPP/Mg2+ | 20.6/20.1 | 29.8/28.6 | 38.3/36.3 | 16.6/14.5 | 12.4/10.1 |
| Water/glycerol | 34.1/25.0 | 39.7/36.9 | 38.1/22.0 | 31.4/ - | 32.5/21.5 |
| Root mean square deviations | |||||
| Bonds (Å) | 0.010 | 0.009 | 0.009 | 0.008 | 0.011 |
| Angles (degree) | 1.2 | 1.1 | 1.2 | 1.1 | 1.1 |
| Ramachandran | |||||
| Favored (%) | 97 | 97 | 97 | 97 | 98 |
| Allowed (%) | 3 | 2.5 | 2.8 | 2.5 | 1.5 |
| Outliers (%) | 0 | 0.5 | 0.2 | 0.5 | 0.5 |
| Protein Data Band code | 5DG7 | 5DG8 | 5DG9 | 5DGA | 5DGB |
a Statistics for the highest resolution shell are shown in parentheses.