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
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52981.8-2.5M Na formate, 0.1 MTris-HCl pH 7.5-8.0, 3% methyl pentane diol
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.663α = 90
b = 95.663β = 90
c = 135.897γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2012-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.55135.91000.088.9310.33313302
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.421000.541.4310.23

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1B0W2.382.8529699157599.970.17350.17090.2222RANDOM27.78
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]
1.040.521.04-1.56
RMS Deviations
KeyRefinement 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)
RMS Deviations
KeyRefinement 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)
GENERAL PLANES OTHERS (A)
NON-BONDED CONTACTS REFINED (A)
NON-BONDED CONTACTS OTHERS (A)
NON-BONDED TORSION REFINED (A)
NON-BONDED TORSION OTHERS (A)
H-BOND (X...Y) REFINED (A)
SYMMETRY VDW REFINED (A)
SYMMETRY VDW OTHERS (A)
SYMMETRY H-BOND REFINED (A)
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3776
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata scaling
REFMACphasing