7CFO

Crystal structure of human RXRalpha ligand binding domain complexed with CBTF-EE.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ZQU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72955% [v/v] tacsimateTM [pH 7.0], 0.1 M HEPES [pH 7.0], and 10% [w/v] PEGMME5000
Crystal Properties
Matthews coefficientSolvent content
2.1542.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.757α = 90
b = 99.432β = 98.31
c = 93.598γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2018-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.1547.1495.60.0810.99616.26.548015
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.230.4980.861.7

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 REPLACEMENTTHROUGHOUT5ZQU2.1547.1445567242395.590.222830.220520.26633RANDOM50.897
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.767
r_dihedral_angle_4_deg22.007
r_dihedral_angle_3_deg17.983
r_long_range_B_other10.374
r_long_range_B_refined10.373
r_scangle_other7.997
r_mcangle_it6.564
r_mcangle_other6.564
r_dihedral_angle_1_deg6.375
r_scbond_it5.421
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.767
r_dihedral_angle_4_deg22.007
r_dihedral_angle_3_deg17.983
r_long_range_B_other10.374
r_long_range_B_refined10.373
r_scangle_other7.997
r_mcangle_it6.564
r_mcangle_other6.564
r_dihedral_angle_1_deg6.375
r_scbond_it5.421
r_scbond_other5.42
r_mcbond_it4.743
r_mcbond_other4.731
r_angle_refined_deg2.001
r_angle_other_deg1.314
r_chiral_restr0.232
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6268
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing