3B0W

Crystal structure of the orphan nuclear receptor ROR(gamma)t ligand-binding domain in complex with digoxin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52951.2M Na formate, 3% (v/v) 2-Methyl-2,4-pentanediol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthew coefficientSolvent content
3.2161.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.716α = 90
b = 98.716β = 90
c = 129.176γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2011-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.000Photon FactoryAR-NW12A

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
12.24099.80.05644.911.436249
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)
12.22.281000.474.611.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3L0L2.2203426534265179199.80.213640.213640.211760.24922RANDOM55.015
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]
0.70.350.7-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.938
r_dihedral_angle_4_deg21.212
r_dihedral_angle_3_deg16.985
r_dihedral_angle_1_deg4.652
r_scangle_it3.606
r_scbond_it2.161
r_mcangle_it1.319
r_angle_refined_deg1.258
r_mcbond_it0.663
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.938
r_dihedral_angle_4_deg21.212
r_dihedral_angle_3_deg16.985
r_dihedral_angle_1_deg4.652
r_scangle_it3.606
r_scbond_it2.161
r_mcangle_it1.319
r_angle_refined_deg1.258
r_mcbond_it0.663
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3516
Nucleic Acid Atoms
Solvent Atoms73
Heterogen Atoms110

Software

Software
Software NamePurpose
SERGUIdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling