Table 1.
Summary of KB and MvS structural statistics for bacterial protein Alr2454. This analysis was generated by the PSVS protein nmr structure quality assessment server [10, 14]. These results are adopted from ref. [67].
| Alr2454a | ||
|---|---|---|
| Completeness of resonance assignmentsb: | ||
| Backbone (%) | 99.4 | |
| Side chain (%) | 98.3 | |
| Aromatic (%) | 96.6 | |
| Stereospecific methyl (%) | 100 | |
| Conformationally-restricting restraintsc: | ||
| Distance restraints | ||
| Total | 2478 | |
| intra-residue (i = j) | 688 | |
| sequential (i-j| = 1) | 619 | |
| medium range (1 < |i - j| < 5) | 462 | |
| long range (|i - j| ≥ 5) | 709 | |
| Dihedral angle restraints | 162 | |
| Hydrogen bond restraints | 0 | |
| Disulfide bond restraints | 0 | |
| No. of restraints per residue | 25.5 | |
| No. of long range restraints per residue | 6.8 | |
| Residual restraint violationsc: | ||
| Average no. of distance violations per structure: | ||
| 0.1 - 0.2 Å | 8.75 | |
| 0.2 - 0.5 Å | 1.85 | |
| > 0.5 Å | 0 | |
| Largest distance violation (Å) | 0.35 | |
| Average no. of dihedral angle violations per structure: | ||
| 1 - 10° | 8.75 | |
| ° 10° | 0 | |
| Largest dihedral angle violation (°) | 3.8 | |
| NOE Completeness Score | 0.692 | |
| Model Qualityc: | ||
| RMSD backbone atoms (Å)d | 0.6 | |
| RMSD heavy atoms (Å)d | 0.9 | |
| RMSD bond lengths (Å) | 0.018 | |
| RMSD bond angles (°) | 1.1 | |
| MolProbity Ramachandran statisticsc,d | ||
| most favored regions (%) | 96.8 | |
| allowed regions (%) | 3.1 | |
| disallowed regions (%) | 0.1 | |
| Global quality scores (Raw / Z-score)c | ||
| Verify3D | 0.40 | −0.96 |
| ProsaII | 0.66 | 0.04 |
| ProCheck (phi-psi)d | −0.15 | −0.28 |
| ProCheck (all)d | −0.03 | −0.18 |
| MolProbity clash score | 12.51 | −0.62 |
| RPF Scorese | ||
| Recall / Precision | 0.976 | 0.934 |
| F-measure / DP-score | 0.955 | 0.817 |
| Model Contents: | ||
| Ordered residue ranged | 1-100 | |
| Total no. of residues | 108 | |
| BMRB accession number: | 17965 | |
| PDB ID: | 2LJW a | |
Structural statistics computed for an ensemble of 20 structures.
Computed using AVS software [68] from the expected number of assignable resonances, excluding: highly exchangeable protons (N-terminal and Lys amino groups, Arg guanido groups, hydroxyls of Ser, Thr, Tyr), carboxyls of Asp and Glu, non-protonated aromatic carbons, and the C-terminal His6 tag. Methyl protons are counted as a single assignable resonance.
Calculated using PSVS 1.4 [10]. Ramachandran statistics were calculated by Molprobity [11]. Average distance violations were calculated using the sum over r−6 for degenerate protons and stereochemically-distinct protons lacking stereospecific assignments.
Based on “well defined” residue ranges [S(phi) + S(psi) > 1.8].