TABLE 2.
Crystal data, data collection parameters, and structure refinement statistics
| Complex |
||||||
|---|---|---|---|---|---|---|
| pol ι(26–445) G·dCMPNPP (Mg2+) | pol ι(26–445) G·dCMPNPP (Mn2+) | pol ι(1–445) G·dCMPNPP (Mg2+) | pol ι(1–445) G·dCMPNPP (Mn2+) | R96G pol ι(1–445) G·dCMPNPP (Mg2+) | R96G pol ι(1–445) G·dCMPNPP (Mn2+) | |
| Data collection | ||||||
| Wavelength (Å) | 0.97872 | 0.97872 | 0.97872 | 0.97872 | 0.97872 | 0.97872 |
| Space group | P6522 | P6522 | P6522 | P6522 | P6522 | P6522 |
| Resolution (Å)a | 50.00–2.49 (2.53–2.49) | 50.00–2.64 (2.69–2.64) | 50.00–3.56 (3.62–3.56) | 50.00–3.15 (3.20–3.15) | 50.00–2.78 (2.83–2.78) | 50.00–2.80 (2.85–2.80) |
| Unit cell (a, b, c) (Å) | 97.61, 97.61, 203.00 | 97.83, 97.83, 202.89 | 98.27, 98.27, 201.66 | 97.74, 97.74, 202.01 | 98.12, 98.12, 202.72 | 97.54, 97.54, 202.21 |
| Unit cell (α, β, γ) (°) | 90.00, 90.00, 120.00 | 90.00, 90.00, 120.00 | 90.00, 90.00, 120.00 | 90.00, 90.00, 120.00 | 90.00, 90.00, 120.00 | 90.00, 90.00, 120.00 |
| No. of unique reflectionsa | 20,810 (1006) | 17,727 (847) | 7564 (363) | 10,495 (487) | 15,324 (729) | 14,993 (720) |
| Completeness (%)a | 99.6 (99.4) | 100 (100) | 99.9 (100) | 99.8 (99.6) | 100 (100) | 99.9 (99.9) |
| I/σ(I)a | 36.2 (3.5) | 31.8 (4.0) | 11.6 (2.5) | 22.9 (4.5) | 30.4 (2.8) | 30.1 (3.7) |
| Wilson B-factor (Å2) | 32.2 | 33.7 | 62.1 | 40.0 | 46.7 | 41.9 |
| Rmergea,b | 0.121 (0.914) | 0.090 (0.784) | 0.222 (0.990) | 0.180 (0.811) | 0.100 (0.922) | 0.117 (0.842) |
| Redundancya | 21.3 (22.0) | 21.2 (21.8) | 14.9 (14.4) | 20.8 (21.1) | 17.7 (17.4) | 21.0 (21.3) |
| Refinement | ||||||
| Rwork | 0.220 | 0.204 | 0.204 | 0.202 | 0.217 | 0.224 |
| Rfree | 0.249 | 0.248 | 0.244 | 0.236 | 0.250 | 0.266 |
| No. of atoms | ||||||
| Protein/DNA | 2941/345 | 2934/345 | 2928/329 | 2926/345 | 2890/345 | 2887/345 |
| dNTP/Metal ions | 28/3c | 28/3c | 28/2 | 28/2 | 28/1 | 28/2 |
| Water | 85 | 65 | 0 | 0 | 22 | 10 |
| B-factor (Å2) | ||||||
| Average | 53.9 | 51.6 | 68.9 | 46.4 | 65.0 | 51.4 |
| Protein/DNA | 54.9/50.4 | 52.5/47.3 | 69.5/64.9 | 47.2/41.0 | 65.4/63.9 | 51.9/49.6 |
| dNTP/Metal ions | 34.9/36.7 | 32.4/59.0 | 54.3/44.9 | 26.3/43.9 | 47.8/40.7 | 31.6/30.6 |
| Water | 42.6 | 41.1 | − | − | 48.7 | 34.1 |
| Root mean square deviations | ||||||
| Bonds (Å) | 0.005 | 0.009 | 0.003 | 0.004 | 0.003 | 0.003 |
| Angles (°) | 0.886 | 1.024 | 0.633 | 0.676 | 0.653 | 0.629 |
| Ramachandran | ||||||
| Favored (%) | 98.7 | 97.9 | 97.1 | 97.3 | 98.4 | 97.6 |
| Allowed (%) | 1.1 | 1.9 | 2.9 | 2.7 | 1.6 | 2.4 |
| Outliers (%) | 0.3 | 0.3 | 0.0 | 0.0 | 0.0 | 0.0 |
| PDB code | 5KT2 | 5KT3 | 5KT6 | 5KT7 | 5KT4 | 5KT5 |
a Values for highest resolution shell are given in parentheses.
b Rmerge: Rlinear = SUM(ABS(I − 〈I〉))/SUM(I), where I is the integrated intensity of a given reflection.
c One non-catalytic metal ion is present in the structure.