3A2J

Crystal structure of the human vitamin D receptor (H305F/H397F) ligand binding domain complexed with TEI-9647


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M MES, pH 6.5, 1.2-1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5451.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.687α = 90
b = 51.393β = 90
c = 131.846γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-10-17MSINGLE 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
12.75099.60.09920.63.7885221
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)
2.72.899.20.3245.623.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1DB12.742.3338852835841599.530.227190.225260.2674RANDOM21.655
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]
0.04-0.090.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.363
r_dihedral_angle_3_deg14.21
r_dihedral_angle_4_deg12.961
r_dihedral_angle_1_deg3.909
r_angle_refined_deg1.079
r_scangle_it0.73
r_mcangle_it0.545
r_scbond_it0.416
r_mcbond_it0.306
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.363
r_dihedral_angle_3_deg14.21
r_dihedral_angle_4_deg12.961
r_dihedral_angle_1_deg3.909
r_angle_refined_deg1.079
r_scangle_it0.73
r_mcangle_it0.545
r_scbond_it0.416
r_mcbond_it0.306
r_nbtor_refined0.294
r_nbd_refined0.168
r_symmetry_vdw_refined0.154
r_symmetry_hbond_refined0.095
r_xyhbond_nbd_refined0.083
r_chiral_restr0.06
r_bond_refined_d0.006
r_gen_planes_refined0.002
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 Atoms2015
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms31

Software

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