7YSE
Crystal structure of E. coli heterotetrameric GlyRS in complex with tRNA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 281 | 0.15M MgCl2, 0.1M NaCl, 0.1M Tris-HCl pH 8.5, 30% PEG 300 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.73 | 67.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.71 | α = 90 |
b = 162.123 | β = 90 |
c = 324.09 | γ = 90 |
Symmetry | |
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Space Group | P 2 2 21 |
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 | 2021-12-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL02U1 | 0.979 | SSRF | BL02U1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.907 | 162.12 | 100 | 0.138 | 0.059 | 0.99 | 9.4 | 6.6 | 85473 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.907 | 3.06 | 0.749 | 0.304 | 0.774 |
Refinement
Statistics | |||||||||||||||||||
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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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7eiv, 4mgm | 2.907 | 50.005 | 85392 | 4393 | 99.885 | 0.231 | 0.2296 | 0.2598 | 77.244 |
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] | |
6.585 | -2.903 | -3.682 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.037 |
r_dihedral_angle_4_deg | 18.004 |
r_dihedral_angle_3_deg | 16.983 |
r_lrange_it | 5.745 |
r_lrange_other | 5.745 |
r_dihedral_angle_1_deg | 5.556 |
r_scangle_it | 3.494 |
r_scangle_other | 3.493 |
r_mcangle_other | 3.475 |
r_mcangle_it | 3.474 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14340 |
Nucleic Acid Atoms | 2952 |
Solvent Atoms | 14 |
Heterogen Atoms | 62 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
autoPROC | data reduction |
Aimless | data scaling |
MOLREP | phasing |