2PID
Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1VBM | PDB ENTRY 1VBM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | 293 | 3 mg/ml protein, 30% (m/v) PEG 4000, 200 mM Ammonium acetate, 100 mM sodium acetate pH 4.6, 100 mM Tris-HCl pH 7.5, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.50 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.05 | 40.01 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 54 | ¦Á = 90 |
b = 62.4 | ¦Â = 90 |
c = 194.6 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 110 | CCD | ADSC QUANTUM 315 | 2006-09-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.2 | 20 | 99.5 | 0.098 | 0.098 | 19.1 | 11.8 | 34168 | -3 | 39.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.2 | 2.3 | 100 | 0.427 | 0.427 | 8.2 | 12.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 1VBM | 2.2 | 19.98 | 34156 | 34156 | 1700 | 99.6 | 0.193 | 0.193 | 0.244 | RANDOM | 40.4 |
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] | |
7.6 | 3.12 | -10.72 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.7 |
c_scangle_it | 5.8 |
c_scbond_it | 4.2 |
c_mcangle_it | 3.84 |
c_mcbond_it | 2.83 |
c_improper_angle_d | 1.71 |
c_angle_deg | 1.4 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5102 |
Nucleic Acid Atoms | |
Solvent Atoms | 90 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
XDS | data reduction |
XSCALE | data scaling |
AMoRE | phasing |