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Crystal structure of the human vitamin D receptor ligand binding domain complexed with 7,8-cis-1a,25-Dihydroxy-19-norvitamin D3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 0.1M MES, pH6.5, 1.2-1.6M ammonium sulfate, VAPOR DIFFUSION, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.55 51.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.819 α = 90 b = 51.27 β = 90 c = 132.166 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 2013-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95370 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.93 47.8 78.2 2 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2.03 24.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.93 42.48 17506 939 78.01 0.17918 0.1769 0.1875 0.22129 0.2322 RANDOM 18.734
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] -0.55 -0.38 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.625 r_dihedral_angle_4_deg 19.651 r_dihedral_angle_3_deg 17.272 r_dihedral_angle_1_deg 6.946 r_angle_refined_deg 2.116 r_angle_other_deg 1.004 r_chiral_restr 0.129 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.625 r_dihedral_angle_4_deg 19.651 r_dihedral_angle_3_deg 17.272 r_dihedral_angle_1_deg 6.946 r_angle_refined_deg 2.116 r_angle_other_deg 1.004 r_chiral_restr 0.129 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2022 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 29
Software Software Software Name Purpose XDS data scaling MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling