Table 1.
Structural statistics for the Pitx2 homeodomain structure ensembles (n=20)
| Wild-type | R24H mutant | |
|---|---|---|
| NMR constraints | ||
| Distance total | 871 | 1467 |
| Intra-residue (i=j) | 253 | 402 |
| Sequential (|i–j|=1) | 229 | 376 |
| Medium range (1 < |i–j| ≤ 4) | 263 | 420 |
| Long range (|i–j| ≥ 5) | 126 | 269 |
| Dihedral angles (ϕ and ψ) | 80 | 98 |
| Amber constraint violations | ||
| Average number of distance constraint violations per structure | ||
| 0.1Å < d < 0.2Å | 0 | 0.25 |
| 0.2Å < d | 0 | 0 |
| Maximum average distance violation (Å) | 0.093 | 0.156 |
| Average number of dihedral angle violations per structure (θ > 0°) | 0 | 0 |
| Maximum average dihedral angle violation (degrees) | 0 | 0 |
| Ensemble superposition statistics (Å)a | ||
| All (residues 1–60) | ||
| Backbone atoms | 8.34 ± 0.23 (3.32) | 4.47 ± 0.05 (1.78) |
| Heavy atoms | 8.43 ± 0.29 (3.36) | 4.44 ± 0.06 (1.77) |
| Well-ordered regions (residues 8–58) | ||
| Backbone atoms | 1.33 ± 0.20 (0.53) | 0.61 ± 0.05 (0.24) |
| Heavy atoms | 1.89 ± 0.24 (0.75) | 1.01 ± 0.05 (0.40) |
| AMBER energies (kcal mol−1) | ||
| Constraint | 1.320 ± 0.132 | 5.036 ± 0.269 |
| van der Waals | −499.1 ± 9.2 | −502.4 ± 6.6 |
| Total | −4316.4 ± 16.5 | −4095.4 ± 12.2 |
| MolProbity statisticsb | ||
| MolProbity score | 1.20 ± 0.30 | 1.16 ± 0.15 |
| MolProbity percentile rank | 97.70 ± 3.24 | 99.10 ± 1.18 |
| Clash score | 0.21 ± 0.36 | 0.09 ± 0.26 |
| Clash score percentile | 99.75 ± 0.43 | 99.90 ± 0.30 |
| Ramachandran space (%) | ||
| Favored | 96.31 ± 2.68 | 98.44 ± 1.31 |
| Allowed | 2.69 ± 2.06 | 1.09 ± 1.22 |
| Outliers | 1.00 ± 1.22 | 0.47 ± 0.72 |
a
Ensemble superposition statistics were calculated using THESEUS, reported as classical least squares pairwise <RMSD> ± ML<σ> (LS<σ>)
b
MolProbity clash score is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms. Clash score percentile: 100th is the best among structures of comparable resolution, whereas 0th is the worst.