1H4Q
Prolyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG), ATP and prolinol
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1HC7 | PDB ENTRY 1HC7 (LIGAND FREE PROLYL-TRNA SYNTHETASE) |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7.9 | SEE REFERENCE 3, pH 7.90 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.42 | 72 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 141.29 | α = 90 |
| b = 141.29 | β = 90 |
| c = 237.56 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | IMAGE PLATE | MARRESEARCH | 1998-06-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID2 | ESRF | ID2 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
| 1 | 3 | 20 | 99.6 | 0.067 | 3.8 | 48648 | |||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 3 | 3.08 | 100 | 0.269 | 2.7 | 3.5 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1HC7 (LIGAND FREE PROLYL-TRNA SYNTHETASE) | 3 | 20 | 48593 | 2452 | 99.8 | 0.221 | 0.221 | 0.254 | RANDOM | |||||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| 0.421 | 0.421 | -0.843 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_scangle_it | 5.82 |
| c_mcangle_it | 3.78 |
| c_scbond_it | 3.5 |
| c_mcbond_it | 2.13 |
| c_angle_deg | 1.392 |
| c_bond_d | 0.007 |
| c_bond_d_na | |
| c_bond_d_prot | |
| c_angle_d | |
| c_angle_d_na | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7479 |
| Nucleic Acid Atoms | 1436 |
| Solvent Atoms | 24 |
| Heterogen Atoms | 88 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CNS | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| AMoRE | phasing |
