5XIH
Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with inhibitor 5
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4TWA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 10%(w/v) PEG 8K, 20%(v/v) ethylene glycol, 0.03M of each divalent cation and 0.1M MOPS/HEPES-Na |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.67 | 53.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.71 | α = 89.71 |
b = 90.763 | β = 80.58 |
c = 93.034 | γ = 75.77 |
Symmetry | |
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Space Group | P 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 | CCD | MARMOSAIC 225 mm CCD | 2015-03-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.9797 | ESRF | BM14 |
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 | 2.2 | 50 | 98.5 | 0.02 | 0.024 | 0.014 | 13.5 | 2.8 | 118866 |
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 | 2.24 | 97.4 | 0.19 | 0.24 | 0.144 | 0.917 | 2.8 |
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 | 4TWA | 2.2 | 47.06 | 112882 | 5984 | 98.3 | 0.1789 | 0.1764 | 0.2256 | RANDOM | 31.481 |
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] | |
-0.49 | 0.01 | -0.01 | 0.16 | 0.04 | 0.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.282 |
r_dihedral_angle_4_deg | 16.356 |
r_dihedral_angle_3_deg | 14.365 |
r_dihedral_angle_1_deg | 6.397 |
r_angle_refined_deg | 1.532 |
r_chiral_restr | 0.104 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15351 |
Nucleic Acid Atoms | |
Solvent Atoms | 670 |
Heterogen Atoms | 324 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data reduction |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data scaling |
PHASER | phasing |