7EIV
heterotetrameric glycyl-tRNA synthetase from Escherichia coli
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.8 | 291 | 0.4 M magnesium acetate, 0.1 M HEPES pH 6.8, 2% (v/v) PEG 3350, 2% (v/v) PEG 5000 MME, 2% (v/v) PEG 4000, 2% (v/v) PEG 2000 and 10% ethylene glycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.47 | 72.47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 207.371 | α = 90 |
b = 253.945 | β = 90 |
c = 270.738 | γ = 90 |
Symmetry | |
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Space Group | F 2 2 2 |
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 | 100 | PIXEL | DECTRIS PILATUS3 6M | 2019-12-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL19U1 | 0.97918 | SSRF | BL19U1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.68 | 50 | 100 | 0.084 | 0.087 | 0.024 | 9.4 | 13.5 | 99458 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.68 | 2.78 | 100 | 0.602 | 0.627 | 0.173 | 0.963 | 13.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.68 | 48.58 | 94460 | 4996 | 99.78 | 0.2293 | 0.2282 | 0.2487 | RANDOM | 68.394 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.17 | -4.98 | 5.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.946 |
r_dihedral_angle_4_deg | 15.958 |
r_dihedral_angle_3_deg | 15.268 |
r_dihedral_angle_1_deg | 5.584 |
r_angle_other_deg | 2.285 |
r_angle_refined_deg | 1.21 |
r_chiral_restr | 0.041 |
r_bond_other_d | 0.035 |
r_gen_planes_other | 0.004 |
r_bond_refined_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13251 |
Nucleic Acid Atoms | |
Solvent Atoms | 56 |
Heterogen Atoms | 76 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
CRANK2 | phasing |