Table 1.
Structure statistics for the Npl4 NZF/Ub complex
| 〈TAD〉a | 〈CNS〉a | |
|---|---|---|
| NOE distance restraintsb (Å) | 2072 | 2072 |
| Npl4 NZF | 478 | 478 |
| Ub | 1485 | 1485 |
| Intermolecular | 109 | 109 |
| Intraresidue | 400 | 400 |
| Sequential (∣i−j∣=1) | 532 | 532 |
| Medium range (2⩽∣i−j∣⩽5) | 388 | 388 |
| Long range (∣I−j∣>5) | 677 | 677 |
| Zinc coordination restraints | 14 | 14 |
| Hydrogen bond distance restraintsc (Å) | 104 | 104 |
| Hydrogen bondsd | 48(4) | 48(4) |
| Dihedral restraintsd | 112(33) | 112(33) |
| DYANA target function (Å2)e | 0.8±0.09 | NA |
| CNS energy (kcal/mol)e | ∼300f | 134.7±4.9 |
| Residual distance restraint violations | ||
| Number of violations ⩾0.1 Å | 0±0 | 0.0 |
| Sum of violations (Å or kcal/mol)e | 1.7±0.1 | 27.0±1.0 |
| Maximum violation (Å) | 0.14 | <0.1 |
| Residual dihedral restraint violations | ||
| Number of violations ⩾1° | NA | 0.0 |
| Sum of violations (deg or kcal/mol)e | NA | 1.29±0.8 |
| Maximum violation (deg) | NA | <2 |
| Van der Waals violations | ||
| Number ⩾0.1 Å | 0±0 | 0.0 |
| Sum of violations (Å or kcal/mol)e | 0.7±0.1 | 34.5±1.7 |
| Maximum violation (Å) | 0.09 | <0.1 |
| Ramachandran statistics (Ub)g | ||
| Favored | 87.3(94.6)% | 84.5(93.2)% |
| Allowed | 11.3(3.8)% | 14.4(5.1)% |
| Generously allowed | 1.3(1.5)% | 1.1(1.7)% |
| Disallowed | 0.0(0.0)% | 0.0(0.0)% |
| Ramachandran statistics (Npl4 NZF)g | ||
| Favored | 59.8% | 68.6% |
| Allowed | 34.5% | 31.4% |
| Generously allowed | 2.6% | 0.0% |
| Disallowed | 3.1% | 0.0% |
| rmsds from the average coordinatesh (Å) | ||
| Secondary elements (backbone, Ub)i | 0.23±0.06 | 0.29±0.08 |
| Secondary elements (heavy atoms, Ub) | 0.85±0.13 | 0.82±0.12 |
| Backbone (complex)j | 0.31±0.07 | 0.35±0.09 |
| Heavy atoms (complex) |
0.92±0.12 |
0.92±0.12 |
| a〈TAD〉 is the ensemble of 40 lowest-penalty structures calculated using the program DYANA. 〈CNS〉 is the same ensemble after 1000 steps (15 ps each) of simulated annealing at 25 K, 1000 slow-cooling steps to 0 K, and 10 000 steps of restrained Powell minimization in Cartesian space (anneal.inp protocol). | ||
| bOnly meaningful and nonredundant restraints as determined by the DYANA CALIBA function. | ||
| cTwo upper-limit distance restraints were used to define each hydrogen bond. | ||
| dHydrogen-bonding and dihedral restraints are reported separately for Ub (no parentheses) and NZF (parentheses). | ||
| eViolation energies from DYANA have units of (Å2) or deg, while energies from CNS are in kcal/mol. | ||
| fEnergies for structures input into CNS (from DYANA) were estimated within the generate_easy.inp program after the first regularization without restraints. | ||
| gDetermined using PROCHECK-NMR. | ||
| hSuperposition and overall rmsds were calculated using the program MOLMOL and PROCHECK_NMR. | ||
| iSecondary elements in Ubiquitin (2–6, 12–16, 22–35, 37–39, 41–45, 48–49, 56–60, and 66–71). | ||
| jAll nondisordered residues (NZF: 5–30; Ub: 1–71). | ||
| NA: not applicable. | ||