TABLE 1.
Summary of structural statistics for the structural refinement using RDCs of the ZZ domain and SUMO1 as well as structural statistics of the docked ZZ domain-SUMO1 complex
Structural analysis was performed using PSVS (29) and PALES (30). The magnitude and orientation of the RDC alignment tensor for the ZZ domain and SUMO1 and the ZZ domain-SUMO1 complex were calculated using Module (45).
| NMR and refinement statistics | Protein |
ZZ domain-SUMO1 complex | |
|---|---|---|---|
| ZZ domain | SUMO1 | ||
| NMR distance and dihedral constraints | |||
| Distance constraints | |||
| Total NOE | 547 | 3304 | |
| Intra-residue | 135 | 476 | |
| Inter-residue | |||
| Sequential (|i − j| = 1) | 172 | 1073 | |
| Medium range (|i − j| <4) | 78 | 644 | |
| Long range (|i − j| >5) | 162 | 1111 | |
| Intermolecular, hydrogen bonds | 5 | 0 | |
| Total dihedral angle restraints | 80 | 0 | |
| Residual dipolar coupling restraints | 42 | 37 | 79 |
| AIR restraintsa | 7 | ||
| Magnitude (Da) | 6.03 | 5.95 | 5.89 |
| Rhombicity | 0.56 | 0.536 | 0.56 |
| Q-factor | 0.30 | 0.26 | 0.36 |
| Structure statistics violations (RMS) | |||
| Distance constraints (Å) | 0.08 Å | 0.05 Å | |
| Dihedral angle constraints (°) | 1.73° | ||
| Max. dihedral angle violation (°) | 8.60° | ||
| Max. distance constraint violation (Å) | 0.55 Å | 0.77 Å | |
| Structure quality factors; overall statistics | |||
| Procheck G-factor (φ/ψ only) | −1.18 | −0.65 | −0.83 |
| Procheck G-factor (all dihedral angles) | −1.04 | −0.39 | −0.56 |
| Verify three-dimensional | 0.27 | 0.30 | 0.29 |
| ProsaII (−ve) | −0.08 | 0.41 | −0.29 |
| MolProbity clash score | 64.01 | 43.88 | 54.67 |
| Ramachandran plot summary from Procheck | |||
| Most favored regions (%) | 63.3 | 70.0 | 77.6 |
| Additionally allowed regions (%) | 30.6 | 22.2 | 15.1 |
| Generously allowed regions (%) | 2.0 | 4.4 | 7.2 |
| Disallowed regions (%) | 4.1 | 3.3 | 0.1 |
a AIR restraints indicate the ambiguous restraints used in the HADDOCK docking procedure.