7OSZ
Human Prolyl-tRNA Synthetase in Complex with L-proline and Compound 4d
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5VAD |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 7.5 | 293 | The purified protein at 30 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was incubated with 10 mM L-proline, 2 mM compound and 12% (v/v) DMSO on ice for 1 hr. Crystals were grown in a Terasaki Microbatch plate by mixing 1 uL the pre-mix with 1 uL of reservoir solution containing 0.25-0.4 M SrCl2, 15-20% (v/v) PEG3350 and 100 mM HEPES pH 7.5. The drops were covered with paraffin oil. Crystals were flash frozen in liquid nitrogen directly from the plate. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.03 | 39.37 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 69.671 | α = 90 |
b = 86.696 | β = 110.14 |
c = 83.117 | 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 PILATUS3 6M | 2018-12-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.976251 | ESRF | ID30B |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.46 | 78.03 | 99.6 | 0.107 | 0.126 | 0.065 | 0.996 | 7 | 3.7 | 33733 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.46 | 2.59 | 99.8 | 0.86 | 1.003 | 0.509 | 0.727 | 3.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5VAD | 2.46 | 78.03 | 1.35 | 33693 | 1724 | 99.48 | 0.223 | 0.2201 | 0.2777 | 62.8381 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 7505 |
Nucleic Acid Atoms | |
Solvent Atoms | 80 |
Heterogen Atoms | 61 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |