1S0X

Crystal structure of the human RORalpha ligand binding domain in complex with cholesterol sulfate at 2.2A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N83PDB ENTRY 1N83

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5277PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7855.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.4α = 90
b = 49.9β = 97.8
c = 60.7γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.9200SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.22099.70.0790.07916.23.5165411654132.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.2899.4

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1N832.220156711567183099.570.197340.197340.196720.20874RANDOM35.919
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]
2-0.79-0.15-2.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.222
r_scangle_it4.207
r_dihedral_angle_1_deg3.301
r_scbond_it2.509
r_mcangle_it1.669
r_angle_refined_deg1.398
r_mcbond_it0.833
r_angle_other_deg0.743
r_symmetry_hbond_refined0.392
r_xyhbond_nbd_other0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.222
r_scangle_it4.207
r_dihedral_angle_1_deg3.301
r_scbond_it2.509
r_mcangle_it1.669
r_angle_refined_deg1.398
r_mcbond_it0.833
r_angle_other_deg0.743
r_symmetry_hbond_refined0.392
r_xyhbond_nbd_other0.323
r_symmetry_vdw_other0.31
r_nbd_refined0.255
r_xyhbond_nbd_refined0.232
r_symmetry_vdw_refined0.213
r_nbd_other0.209
r_chiral_restr0.079
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2066
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CCP4data scaling