Table 1.
Data collection and model refinement statistics
| DUT1 (apo structure) (PDB code 3HHQ) | DUT1 (+α,β-imido dUTP) (PDB code 3P48) | DUT1 (+dUMP) (PDB code 3F4F) | |
|---|---|---|---|
| Data collection | |||
| Space group | P1 | P212121 | P43212 |
| Cell dimensions | |||
| a,b,c (Å) | 95.5, 95.5, 97.6 | 51.7, 58.8, 112.3 | 124.5, 124.5, 51.7 |
| α,β,γ (°) | 98.8, 97.4, 107.1 | 90.0, 90.0, 90.0 | 90.0, 90.0, 90.0 |
| Wavelength | 1.541 | 0.979 | 1.541 |
| Resolution (Å) | 50.0–2.0 (2.07–2.0) | 28.47–1.67 (1.76–1.67) | 50–2.0 (2.07–2.0) |
| Reflections overall (outer shell) | 191 238 (19074) | 40 597 (5802) | 53 958 (5381) |
| R merge | 0.058 (0.441) | 0.043 (0.239) | 0.086 (0.386) |
| I/σ/ | 19.1 (3.4) | 28.4 (8.2) | 15.1 (4.9) |
| Completeness (%) | 89.2 (88.3) | 99.9 (99.8) | 99.9 (100) |
| Redundancy | 3.4 (3.2) | 6.3 (6.1) | 4.3 (4.0) |
| Refinement | |||
| Resolution (Å) | 40.62–2.0 | 28.47–1.67 | 47.7–2.0 |
| Number of reflections* | 181642 (9588) | 40 218 (2017) | 26 589 (1406) |
| Rwork/Rfree | 0.175/0.236 | 0.154/0.192 | 0.146/0.207 |
| Number of atoms | |||
| Protein | 23034 | 3326 | 3147 |
| Major ligand | – | 126 (42×3) | 60 |
| Solvent | 1765 | 405 | 437 |
| Other | 363 | 3 | 23 |
| Rmsd | |||
| Bond lengths (Å) | 0.021 | 0.017 | 0.015 |
| Bond angles (°) | 1.85 | 1.656 | 1.66 |
| Ramachandran plot | |||
| Most favoured (%) | 90.0 | 98.7 | 92.3 |
| Additionally allowed (%) | 8.1 | 1.3 | 6.9 |
| Disallowed (%) | 0.2 | 0.0 | 0.9 |
Values in parentheses are for the highest-resolution shell.
*
Number of reflections overall and in the test set.