6CN5
HUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA LIGAND- BINDING DOMAIN IN COMPLEX WITH INDOLE LIGAND CP9b IN INVERSE AGONIST CONFORMATION
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.5 | 298 | 1.8-2.5M Na formate, 0.1 MTris-HCl pH 7.5-8.0, 3% methyl pentane diol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.663 | α = 90 |
b = 95.663 | β = 90 |
c = 135.897 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 PILATUS3 6M | 2012-03-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.0 | APS | 17-ID |
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 | 1.55 | 135.9 | 100 | 0.08 | 8.93 | 10.33 | 31330 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.3 | 2.42 | 100 | 0.54 | 1.43 | 10.23 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1B0W | 2.3 | 82.85 | 29699 | 1575 | 99.97 | 0.1735 | 0.1709 | 0.2222 | RANDOM | 27.78 |
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] | |
1.04 | 0.52 | 1.04 | -1.56 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
TORSION ANGLES, PERIOD 3 (DEGREES) | 19.987 |
TORSION ANGLES, PERIOD 1 (DEGREES) | 5.647 |
BOND ANGLES REFINED (DEGREES) | 2.021 |
CHIRAL-CENTER RESTRAINTS (A**3) | 0.148 |
BOND LENGTHS REFINED (A) | 0.023 |
GENERAL PLANES REFINED (A) | 0.009 |
BOND LENGTHS OTHERS (A) | |
BOND ANGLES OTHERS (DEGREES) | |
TORSION ANGLES, PERIOD 2 (DEGREES) | |
TORSION ANGLES, PERIOD 4 (DEGREES) |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3776 |
Nucleic Acid Atoms | |
Solvent Atoms | 100 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
autoPROC | data scaling |
REFMAC | phasing |