3V1T
Crystal structure of a putative ketoacyl reductase (FabG4) from Mycobacterium tuberculosis H37Rv at 1.9 Angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3Q6I | PDB ENTRY 3Q6I |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 300 | 45%(v/v) polypropylene glycol, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.388 | α = 99.24 |
b = 57.594 | β = 102.98 |
c = 71.488 | γ = 117.04 |
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 | 103 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2011-12-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | 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 | 1.876 | 66.392 | 91 | 0.057 | 8 | 1.9 | 56389 | 56389 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.88 | 1.98 | 73.3 | 0.372 | 0.372 | 0.527 | 0.372 | 2.1 | 1.8 | 6666 |
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 | PDB ENTRY 3Q6I | 1.88 | 66.39 | 56360 | 2284 | 90.91 | 0.1834 | 0.1805 | 0.2525 | RANDOM | 26.298 |
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] | |
2.27 | 1.79 | 1.54 | 0.25 | 1.35 | 0.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.344 |
r_dihedral_angle_4_deg | 21.224 |
r_dihedral_angle_3_deg | 14.917 |
r_dihedral_angle_1_deg | 6.486 |
r_scangle_it | 4.33 |
r_scbond_it | 2.884 |
r_angle_refined_deg | 1.833 |
r_mcangle_it | 1.653 |
r_mcbond_it | 1.082 |
r_chiral_restr | 0.123 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5826 |
Nucleic Acid Atoms | |
Solvent Atoms | 664 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
StructureStudio | data collection |
XSCALE | data scaling |
PHASER | phasing |