Crystal structure of Escherichia coli trptophanyl-tRNA synthetase in complex with N-piperidine ibrutinib
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8I1Y | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 290 | 0.15 M ammonium sulfate, 0.1M HEPES pH 7.5, 25% w/v PEG 3,350 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.42 | 49.11 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 61.768 | α = 90 |
| b = 79.649 | β = 105.78 |
| c = 78.361 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2023-10-20 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRF BEAMLINE BL02U1 | 0.97918 | SSRF | BL02U1 |
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 | 1.59 | 75.41 | 99.9 | 0.094 | 9 | 5.6 | 98739 | ||||||||||||
| 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 | 1.59 | 1.67 | 1.535 | 1.4 | |||||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 8I1Y | 1.59 | 54.49 | 92139 | 4705 | 98 | 0.18985 | 0.18908 | 0.1961 | 0.20487 | 0.214 | RANDOM | 22.836 | ||||
| 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] | |
| -1.62 | -0.25 | 1.55 | 0.18 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.407 |
| r_dihedral_angle_4_deg | 18.702 |
| r_dihedral_angle_3_deg | 12.118 |
| r_dihedral_angle_1_deg | 5.367 |
| r_long_range_B_refined | 3.848 |
| r_long_range_B_other | 3.814 |
| r_scangle_other | 2.973 |
| r_mcangle_it | 2.084 |
| r_mcangle_other | 2.084 |
| r_scbond_it | 1.954 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4958 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 470 |
| Heterogen Atoms | 92 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| autoPROC | data reduction |
| XDS | data scaling |
| MOLREP | phasing |
