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Crystal structure of the human VDR ligand binding domain bound to the synthetic agonist compound 2alpha-methyl-AMCR277B(C23R)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DB1 PDB ENTRY 1DB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 10mM Tris, 100mM NaCl, 1nM TCEP, 0.05M Mes, 0.7M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.56 51.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.969 α = 90 b = 51.496 β = 90 c = 131.91 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2008-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.975531 ESRF ID29
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.45 50 96 0.053 0.053 22.5 2.4 55357 53143 15.2
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) Redundancy Number Unique Reflections (All) 1 1.45 1.5 97.5 0.317 0.317 2.6 2.4 5293
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DB1 1.45 18.5 55357 50391 2712 96.06 0.16216 0.16038 0.1596 0.19556 0.1952 RANDOM 18.189
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] -0.59 -0.12 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.664 r_dihedral_angle_4_deg 13.869 r_dihedral_angle_3_deg 10.838 r_dihedral_angle_1_deg 4.296 r_scangle_it 3.145 r_scbond_it 2.932 r_sphericity_free 2.807 r_rigid_bond_restr 2.72 r_sphericity_bonded 2.559 r_mcangle_it 1.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.664 r_dihedral_angle_4_deg 13.869 r_dihedral_angle_3_deg 10.838 r_dihedral_angle_1_deg 4.296 r_scangle_it 3.145 r_scbond_it 2.932 r_sphericity_free 2.807 r_rigid_bond_restr 2.72 r_sphericity_bonded 2.559 r_mcangle_it 1.349 r_angle_refined_deg 1.29 r_mcbond_it 0.803 r_nbtor_refined 0.308 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.176 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2026 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing