Table 1.
Summary of X-ray Data Collection and refinement Statistics for Mag2-DNA Complexes
| Crystal | Gua7:Cyt16 | 5-BrU derivative | Cyt7:Gua16 | Ade7:Thy16 | Thy6:Ade16 | ||
|---|---|---|---|---|---|---|---|
| PDB code | 4b21 | 4b22 | 4b23 | 4b24 | |||
| Data collection | |||||||
| Space group | I222 | I222 | I222 | I222 | I222 | ||
| Cell dimensions (Å) | a = 68.93 | a = 67.66 | a = 68.48 | a = 68.88 | a = 68.65 | ||
| b = 84.75 | b = 84.12 | b = 84.52 | b = 84.60 | b = 84.65 | |||
| c = 126.71 | c = 125.41 | c = 125.75 | c = 125.58 | c = 125.96 | |||
| Peak | Inflection | Remote | |||||
| Wavelength (Å) | 1.11 | 0.9203 | 0.9205 | 0.9558 | 0.9200 | 1.5418 | 1.5418 |
| Resolution (Å) | 50 - 1.45 | 50 – 2.8 | 50 – 2.8 | 50 – 2.8 | 50 – 1.9 | 50 – 2.0 | 50.0 – 2.3 |
| Wilson B-factor | 28.2 | 22.7 | 29.8 | 27.3 | |||
| Rsyma | 0.075 (0.44) | 0.047 (0.10) | 0.047 (0.10) | 0.042 (0.076) | 0.061 (0.315) | 0.089 (0.21) | 0.13 (0.36) |
| I/σI | 15.2 (4.3) | 23.6 (11.2) | 23.9 (11.4) | 27.6 (14.9) | 16.2 (4.3) | 8.4 (2.7) | 4.9 (1.8) |
| Completeness (%) | 100 (100) | 99.5 (100) | 99.5 (100) | 99.5 (100) | 99.3 (96.0) | 94.4 (93.9) | 99.5 (99.3) |
| Redundancy | 6.9 (4.6) | 4.3 (4.3) | 4.3 (4.3) | 4.3 (4.3) | 4.3 (3.8) | 3.7 (3.7) | 3.4 (3.4) |
| Figure of merit, Resolve | 0.68 | ||||||
| Refinement | |||||||
| Resolution (Å) | 50 – 1.45 | 50 – 1.9 | 50 – 2.0 | 50 – 2.3 | |||
| No. reflections | 59374 | 26375 | 21185 | 15169 | |||
| Rwork/Rfreeb | 0.21/0.22 | 0.20/0.23 | 0.25/0.29 | 0.23/0.27 | |||
| No. atoms | |||||||
| Protein | 1688 | 1637 | 1646 | 1646 | |||
| DNA | 418 | 437 | 437 | 418 | |||
| Water | 255 | 245 | 208 | 146 | |||
| Phosphate | 15 | - | - | - | |||
| Glucose | 12 | - | - | - | |||
| B-factors | |||||||
| Protein | 23.2 | 21.5 | 27.2 | 30.6 | |||
| DNA | 30.1 | 31.7 | 35.1 | 35.1 | |||
| Water | 40.6 | 33.0 | 36.4 | 37.0 | |||
| R.m.s. deviation from ideal geometry | |||||||
| bond lengths (Å) | 0.004 | 0.005 | 0.005 | 0.008 | |||
| bond angles (°) | 1.3 | 1.1 | 1.1 | 1.3 | |||
| Ramachandran plot (%) | |||||||
| Best regions | 96.3 | 96.6 | 96.1 | 93.6 | |||
| Disallowed | 0.0 | 0.5 | 0.5 | 0.5 | |||
a
Values in parentheses refer to the highest resolution shells. These are 1.50 - 1.45, 2.89 – 2.8, 2.0 – 1.9, 2.07 – 2.0, and 2.38 – 2.3 Å, respectively.
b
4.8, 4.6, 4.3 and 4.1%, respectively, of randomly distributed data over the full resolution range, were flagged as belonging to the Rfree cross validation set not to be used in the refinement.