5AQC
KstR, transcriptional repressor of cholesterol degradation in Mycobacterium tuberculosis, bound to the cholesterol coenzyme A derivative, (25R)-3-oxocholest-4-en-26-oyl-CoA.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3MNL | PDB ENTRY 3MNL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 11% PEG 3350, 90 MM NASO4, 22% MPD, pH 7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.329 | α = 90 |
b = 67.404 | β = 105.71 |
c = 49.923 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 110 | CCD | MARRESERCH | MIRRORS | 2015-09-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.66 | 61.29 | 92.4 | 0.06 | 8.6 | 3.6 | 44460 | 1.2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.66 | 1.75 | 62.2 | 0.65 | 1.2 | 2.6 |
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 3MNL | 1.66 | 61.29 | 42163 | 2244 | 92.32 | 0.18603 | 0.1838 | 0.22604 | RANDOM | 26.67 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.38 | -0.08 | 0.23 | -1.37 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.355 |
r_dihedral_angle_4_deg | 18.32 |
r_dihedral_angle_3_deg | 14.71 |
r_dihedral_angle_1_deg | 4.934 |
r_mcangle_it | 3.448 |
r_scbond_it | 3.376 |
r_mcbond_it | 2.556 |
r_mcbond_other | 2.538 |
r_angle_refined_deg | 1.94 |
r_angle_other_deg | 0.937 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2726 |
Nucleic Acid Atoms | |
Solvent Atoms | 227 |
Heterogen Atoms | 93 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |