6YJH
Crystal structure of Imidazole Glycerol Phosphate Dehydratase from Mycobacterium tuberculosis at 1.61 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4GQU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | COUNTER-DIFFUSION | 293 | 30% PEG1500, 0.2 M sodium citrate tribasic dehydrate, 0.1 M Tris pH 7.5, 5 mM MnCl2, 0.04% NaN3 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 56.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 112.13 | α = 90 |
b = 112.13 | β = 90 |
c = 112.13 | γ = 90 |
Symmetry | |
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Space Group | P 4 3 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 PILATUS 2M | 2016-06-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 0.8 | SPring-8 | BL41XU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.61 | 30 | 99.09 | 0.099 | 0.1 | 5.9569 | 27.56 | 31512 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.61 | 1.7 | 93.86 | 0.38 | 0.428 | 4.44 |
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 | 4GQU | 1.61 | 29.97 | 29932 | 1574 | 98.96 | 0.1524 | 0.1512 | 0.1748 | RANDOM | 16.033 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.356 |
r_dihedral_angle_4_deg | 16.695 |
r_dihedral_angle_3_deg | 12.65 |
r_dihedral_angle_1_deg | 6.963 |
r_angle_refined_deg | 1.795 |
r_angle_other_deg | 1.588 |
r_chiral_restr | 0.089 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.011 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1476 |
Nucleic Acid Atoms | |
Solvent Atoms | 99 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
iMOSFLM | data reduction |