Table 1.
Statistics of Data Collection and Model Refinement of Human HisRS Crystal and NMR Structures
| Crystal structures of HisRS variants | Family of 20 NMR structures of HisRSΔCD*d | |||
|---|---|---|---|---|
| HisRS Δ507–509 | HisRS Δ1–53_ Δ507–509 | NMR distance and dihedral constraints | ||
| Data collection | Total NOE | 2397 | ||
| Space group | P41212 | P41212 | Intra-residue | 978 |
| Unit cell parameters (Å) | a = b = 100.4, c = 257.1 | a = b = 93.5, c = 254.5 | Inter-residue | |
| Resolution range (Å) | 50 − 3.1 (3.15 − 3.1)a | 50 − 2.4 (2.44 − 2.4) | Sequential (|i − j| = 1) | 491 |
| No. of unique reflections | 24210 (1191) | 45571 (2212) | Medium-range (|i − j| < 4) | 404 |
| Redundancy | 5.5 (5.6) | 6.1 (5.8) | Long-range (|i − j| > 5) | 929 |
| I/σ | 22.6 (2.4) | 21.8 (2.3) | Hydrogen bonds | 148 |
| Completeness (%) | 98.8 (99.9) | 99.8 (99.9) | Total dihedral angle restraints | 216 |
| Rmerge (%)b | 6.9 (69.6) | 7.4 (67.9) | Structure statistics | |
| Structure refinement | Violations (mean and s.d.) | |||
| Resolution (Å) | 50 − 3.1 (3.2 − 3.1) | 50 − 2.4 (2.49 − 2.4) | Distance constraints (Å) | 0.001 ± 0.001 |
| Rcryst / Rfree (%)c | 27.1 (34.4) / 32.7 (40.0) | 19.1 (26.8) / 25.0 (35.1) | Dihedral angle constraints (°) | 0.574 ± 0.063 |
| Rmsd bonds (Å) / angles (°) | 0.014 / 1.5 | 0.005 / 0.9 | Deviations from idealized geometry | |
| Average B factor | 55 | 54.4 | Bond lengths (Å) | 0.002 ± 0.000 |
| No. of atoms | Bond angles (°) | 0.429 ± 0.022 | ||
| Protein atoms | 6430 | 6907 | Impropers (°) | 0.347 ± 0.047 |
| Water molecules | 166 | Ramachandran plote (%) | ||
| Other molecules | 21 | Most favorable regions | 79.7 | |
| No. of reflections | Additional allowed regions | 14.2 | ||
| Working set | 22659 | 42096 | Generously allowed regions | 4.3 |
| Test set | 1213 | 2124 | Disallowed regions | 1.8 |
| Ramachandran plot | Coordinate precision | |||
| Most favored regions (%) | 88.2 | 92.7 | Atomic Rmsdf (Å) | |
| Additionally allowed (%) | 11 | 7.3 | Residues 1–45 for the WHEP domain | |
| Generously allowed (%) | 0.8 | 0 | Heavy | 1.081 |
| Backbone | 0.447 | |||
| Residues 69–165 for the ABD | ||||
| Heavy | 1.468 | |||
| Backbone | 0.872 | |||
Numbers in parentheses represent the value for the highest resolution shell.
Rmerge = Σ|Ii − Im|/ΣIi, where Ii is the intensity of the measured reflection and Im is the mean intensity of all symmetry related reflections.
Rcryst = Σ||Fobs| − |Fcalc||/Σ|Fobs|, where Fobs and Fcalc are observed and calculated structure factors. Rfree = ΣT||Fobs| − |Fcalc||/ΣT|Fobs|, where T is a test data set of about 5% of the total reflections randomly chosen and set aside prior to refinement.
None of the structures exhibits distance violations greater than 0.3 Å or dihedral angle violations greater than 4°.
The program Procheck was used to assess the overall quality of the structures.
The precision of the atomic coordinates is defined as the average Rmsd between 20 final structures and the mean coordinates of the protein.