3R5M

Crystal structure of RXRalphaLBD complexed with the agonist magnolol


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527720% PEG3350, 100 mM Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1342.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.95α = 90
b = 65.83β = 90
c = 110.29γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-05-15MSINGLE 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)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
12.8110.43298.70.0560.05611.83.6118631186322
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.852.999.70.3810.3812.73.6

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 2P1T2.856.6118631176057599.810.251610.249370.29279RANDOM46.513
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]
-0.1-0.120.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.857
r_dihedral_angle_4_deg24.138
r_dihedral_angle_3_deg17.761
r_dihedral_angle_1_deg4.807
r_scangle_it1.133
r_angle_refined_deg1.069
r_scbond_it0.679
r_mcangle_it0.626
r_mcbond_it0.351
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.857
r_dihedral_angle_4_deg24.138
r_dihedral_angle_3_deg17.761
r_dihedral_angle_1_deg4.807
r_scangle_it1.133
r_angle_refined_deg1.069
r_scbond_it0.679
r_mcangle_it0.626
r_mcbond_it0.351
r_nbtor_refined0.3
r_nbd_refined0.204
r_symmetry_vdw_refined0.19
r_xyhbond_nbd_refined0.145
r_symmetry_hbond_refined0.144
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms3557
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms40

Software

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