3R2A

Crystal structure of RXRalpha ligand-binding domain complexed with corepressor SMRT2 and antagonist rhein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NSPPDB ENTRY 3NSP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293100 mM sodium cacodylate, 20% PEG4000, 100 mM magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.03α = 90
b = 117.58β = 90
c = 117.12γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277CCDMARMOSAIC 225 mm CCD2011-01-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17USSRFBL17U

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
1382.979990.08329.83.6241682384322
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)
133.11000.5424.13.8

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3NSP342.52216322163211671000.258120.254150.33492RANDOM71.164
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]
-0.040.06-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.36
r_dihedral_angle_3_deg19.782
r_dihedral_angle_4_deg19.141
r_dihedral_angle_1_deg6.323
r_scangle_it1.449
r_angle_refined_deg1.353
r_mcangle_it0.924
r_scbond_it0.828
r_mcbond_it0.509
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.36
r_dihedral_angle_3_deg19.782
r_dihedral_angle_4_deg19.141
r_dihedral_angle_1_deg6.323
r_scangle_it1.449
r_angle_refined_deg1.353
r_mcangle_it0.924
r_scbond_it0.828
r_mcbond_it0.509
r_nbtor_refined0.31
r_nbd_refined0.234
r_symmetry_vdw_refined0.22
r_xyhbond_nbd_refined0.15
r_symmetry_hbond_refined0.12
r_chiral_restr0.096
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6838
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms42

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling