6WQI
Xanthomonas citri Methionyl-tRNA synthetase (apo)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6WQ6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | 0.1 M Tris-HCl, 28 - 32% PEG4000, 0.2 M MgCl2, 0.45 % Polyvinylpyrrolidone K15 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.91 | 35.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.017 | α = 90 |
b = 95.253 | β = 90.52 |
c = 84.08 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 PILATUS 2M | 2017-04-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE W01B-MX2 | 1.4586 | LNLS | W01B-MX2 |
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) | 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 | 47.83 | 97 | 0.107 | 0.127 | 0.069 | 0.996 | 8.6 | 3.3 | 76238 |
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 | 2.04 | 95 | 0.918 | 1.107 | 0.609 | 0.574 | 3.1 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6WQ6 | 2 | 47.83 | 72445 | 3766 | 94.31 | 0.1874 | 0.185 | 0.2301 | RANDOM | 32.944 |
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] | |
44.92 | 9.17 | -25.19 | -19.74 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.329 |
r_dihedral_angle_4_deg | 19.277 |
r_dihedral_angle_3_deg | 15.978 |
r_dihedral_angle_1_deg | 6.438 |
r_angle_refined_deg | 1.657 |
r_angle_other_deg | 1.437 |
r_chiral_restr | 0.084 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8488 |
Nucleic Acid Atoms | |
Solvent Atoms | 498 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |