Table 1.
Data collection and refinement statistics
| Data collection | Se-Remote (A) | Se-Edge (A) | Se-Peak (A) | Se-Remote (B) | Se-Edge (B) | Se-Peak (B) |
|---|---|---|---|---|---|---|
| Wavelength (Å) | 0.9500 | 0.9790 | 0.9788 | 0.9500 | 0.9789 | 0.9787 |
| Resolution (Å) | 50–2.9 | 50–2.85 | 50–2.8 | 40–3.15 | 40–3.0 | 40–3.1 |
| Number of reflections | ||||||
| Measured | 422 352 | 441 284 | 471 659 | 357 523 | 398 046 | 354 495 |
| Unique | 118 308 | 123 652 | 130 580 | 98 495 | 108 359 | 101 746 |
| Redundancy | 3.6 | 3.6 | 3.6 | 3.7 | 3.6 | 3.6 |
| Completeness (%)a | 99.8 (98.6) | 99.3 (94.5) | 99.8 (98.7) | 99.0 (94.1) | 99.4 (96.3) | 99.5 (97.4) |
| Rmerge (%)b | 7.8 | 8.0 | 8.5 | 11.2 | 9.1 | 10.2 |
| I/σ | 15.55 (2.5) | 14.33 (2.3) | 12.79 (2.9) | 11.37 (2.3) | 13.36 (2.2) | 11.79 (2.4) |
| RCullis c | 0.84 | 0.73 | 0.76 | 0.87 | 0.75 | 0.78 |
| Phasing power | 0.74 | 1.27 | 1.27 | 0.68 | 0.97 | 1.00 |
| Data collection |
Hg-peak |
Pt-peak |
Br-peak |
|||
| Wavelength (Å) | 1.0055 | 1.0711 | 0.9109 | Overall FOMd 0.55/0.88 | ||
| Resolution (Å) | 40–2.9 | 50–3.15 | 40–2.9 | Refinement (against data set Se-peak (A)) | ||
| Number of reflections | Number of atoms | |||||
| Measured | 443 832 | 327 667 | 442 194 | Protein (non-hydrogen) | 29 586 | |
| DNA | 2240 | |||||
| Unique | 118 013 | 90 372 | 118 856 | Water | 213 | |
| Redundancy | 3.8 | 3.6 | 3.7 | Rwork (%)e | 24.6 | |
| Completeness (%) | 99.7 (99.2) | 98.5 (89.8) | 99.2 (98.5) | Rfree (%)e | 29.1 | |
| Rmerge (%) | 6.2 | 7.1 | 8.7 | r.m.s.d. bond distances (Å) | 0.0073 | |
| I/σ | 21.1 (3.3) | 16.2 (2.1) | 14.3 (2.0) | r.m.s.d. bond angles (Å) | 1.22 | |
| Phasing power | 0.08 | 0.19 | 0.04 | |||
| Riso f (%) | 12.4 | 22.5 | 22.5 | |||
| |
Pol1 |
Pol2 |
Exo1 |
Exo2 |
||
| Ramachandran plot | ||||||
| Core region (%) | 84.2 | 84.8 | 74.3 | 63.3 | ||
| Allowed (%) | 14.1 | 14.4 | 22.3 | 33.3 | ||
| Generously allowed (%) | 1.6 | 0.7 | 2.7 | 2.7 | ||
| Disallowed (%) | 0.1 | 0.1 | 0.7 | 0.7 | ||
| Average B factor all atoms (Å2) | ||||||
| Protein only | 49.7 | 42.9 | 65.5 | 95.0 | ||
| DNA only |
54.4 |
89.6 |
96.7 |
110.7 |
|
|
| aThe numbers in parentheses are the statistics for the highest resolution shell. | ||||||
| bRmerge=∑∣I−〈I〉∣/∑I, where 〈I〉 is the average intensity from multiple observations of symmetry-related reflections. | ||||||
| cRCullis=[〈(LOC)2〉]1/2 (〈∣ΔF∣2〉)1/2, where LOC is the lack-of-closure error. | ||||||
| dFigure of merit, before and after density modification. | ||||||
| eRwork and Rfree=∑h∥∣Fo∣−∣Fc∥/∑h∣Fo∣, where Fo and Fc are the observed and calculated structure factor amplitudes. Rfree was calculated with 10% of the reflections not used in refinement. | ||||||
| fRiso=∑∣FPH−FP∣/∑∣FP∣, where FP is the observed structure factor amplitude for the reference data set (Se-peak (A)) and FPH is the observed structure factor amplitude for the heavy atom derivatives. | ||||||