3A3Z

Crystal structure of the human VDR ligand binding domain bound to the synthetic agonist compound 2alpha-methyl-AMCR277A(C23S)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP627710mM Tris, 100mM NaCl, 1nM TCEP, 0.05M Mes, 0.7M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6152.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.297α = 90
b = 51.688β = 90
c = 133.092γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87260ESRFID23-2

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
11.73097.90.0830.08310.42.53354632842
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)
11.71.7695.90.3370.3372.72.2

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 1DB11.72303354631149166496.490.178590.176940.20917RANDOM12.52
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]
-0.030.22-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.374
r_dihedral_angle_4_deg15.355
r_dihedral_angle_3_deg10.997
r_dihedral_angle_1_deg4.029
r_scangle_it1.656
r_angle_refined_deg1.11
r_scbond_it1.062
r_mcangle_it0.697
r_mcbond_it0.443
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.374
r_dihedral_angle_4_deg15.355
r_dihedral_angle_3_deg10.997
r_dihedral_angle_1_deg4.029
r_scangle_it1.656
r_angle_refined_deg1.11
r_scbond_it1.062
r_mcangle_it0.697
r_mcbond_it0.443
r_nbtor_refined0.295
r_nbd_refined0.18
r_symmetry_vdw_refined0.116
r_xyhbond_nbd_refined0.075
r_chiral_restr0.072
r_symmetry_hbond_refined0.069
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 Atoms2026
Nucleic Acid Atoms
Solvent Atoms447
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing