Table 2.
Data collection and refinement statistics
| RNF168 UDM1–K63-Ub2 (form I) | RNF168 UDM1–K63-Ub2 (form II) | RNF168 UDM1–K63-Ub2 (tetrameric form) | RNF168 UDM2ΔC–K63-Ub2 | |
|---|---|---|---|---|
| Data collection | ||||
| Beamline | SPring-8 BL41XU | SPring-8 BL41XU | SPring-8 BL41XU | SPring-8 BL41XU |
| Wavelength (Å) | 1.0000 | 1.0000 | 1.0000 | 1.0000 |
| Space group | P1 | P1 | P21 | P21212 |
| Cell dimensions | ||||
| a, b, c (Å) | 35.3, 66.3, 74.2 | 45.4, 50.0, 64.4 | 85.3, 64.1, 117.5 | 59.4, 78.5, 31.0 |
| α, β, γ (˚) | 76.5, 79.3, 80.5 | 73.5, 69.7, 73.8 | 90.0, 109.6, 90.0 | 90.0, 90.0, 90.0 |
| Resolution (Å) | 50.0–1.78 (1.81–1.78) | 50.0–2.25 (2.29–2.25) | 50.0–2.50 (2.54–2.50) | 50.0–1.80 (1.83–1.80) |
| Completeness (%) | 92.9 (92.0) | 90.2 (91.5) | 97.2 (97.4) | 99.3 (99.2) |
| Redundancy | 6.3 (5.0) | 3.1 (3.0) | 5.1 (4.4) | 7.7 (6.3) |
| I/σI | 32.7 (1.4) | 20.2 (1.8) | 6.9 (1.3) | 20.7 (2.7) |
| Rsym | 0.064 (0.667) | 0.112 (0.670) | 0.128 (0.673) | 0.137 (0.523) |
| Refinement | ||||
| No. of atoms: protein, ligand, water | 3714, 22, 458 | 3649, 33, 58 | 7481, 12, 278 | 985, 20, 151 |
| R.m.s.d. bond length (Å) | 0.005 | 0.003 | 0.004 | 0.006 |
| R.m.s.d. bond angle (˚) | 0.93 | 0.62 | 0.60 | 0.74 |
| Average B-factors (Å2): protein, ligand, water | 47.66, 85.08, 49.19 | 69.56, 87.80, 61.55 | 37.39, 38.15, 35.24 | 20.06, 28.71, 35.32 |
| Ramachandran plot (%): favored, allowed, outliers | 99.6, 0.4, 0.0 | 99.1, 0.9, 0.0 | 99.4, 0.6, 0.0 | 99.1, 0.9, 0.0 |
| Rwork, Rfree | 0.219, 0.245 | 0.220, 0.239 | 0.230, 0.260 | 0.169, 0.207 |
Values in parentheses are for the highest resolution shell