☰ Navigation Tabs
Crystal structure of the human VDR ligand binding domain bound to the synthetic agonist compound 2alpha-methyl-AMCR277A(C23S)
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 2.61 52.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.297 α = 90 b = 51.688 β = 90 c = 133.092 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 MARMOSAIC 225 mm CCD 2009-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.7 30 97.9 0.083 0.083 10.4 2.5 33546 32842
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 1.7 1.76 95.9 0.337 0.337 2.7 2.2
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 1.72 30 33546 31149 1664 96.49 0.17859 0.17694 0.1762 0.20917 0.2069 RANDOM 12.52
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] -0.03 0.22 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.374 r_dihedral_angle_4_deg 15.355 r_dihedral_angle_3_deg 10.997 r_dihedral_angle_1_deg 4.029 r_scangle_it 1.656 r_angle_refined_deg 1.11 r_scbond_it 1.062 r_mcangle_it 0.697 r_mcbond_it 0.443 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.374 r_dihedral_angle_4_deg 15.355 r_dihedral_angle_3_deg 10.997 r_dihedral_angle_1_deg 4.029 r_scangle_it 1.656 r_angle_refined_deg 1.11 r_scbond_it 1.062 r_mcangle_it 0.697 r_mcbond_it 0.443 r_nbtor_refined 0.295 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.116 r_xyhbond_nbd_refined 0.075 r_chiral_restr 0.072 r_symmetry_hbond_refined 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 Atoms Number Protein Atoms 2026 Nucleic Acid Atoms Solvent Atoms 447 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing