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Crystal structure of VDR-LBD complexed with 22S-butyl-25-hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 MOPS-Na, Na-Formate, PEG 4000, Ethylenglycol
Crystal Properties Matthews coefficient Solvent content 2.04 39.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.78 α = 90 b = 44.91 β = 93.62 c = 45.52 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2016-02-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
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 2.05 64.26 88.7 11.3 2.9 14660
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 2.05 64.26 13899 748 88.69 0.18883 0.18607 0.1952 0.24173 0.2535 RANDOM 26.443
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] -0.87 -0.04 0.79 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.433 r_dihedral_angle_3_deg 16.921 r_dihedral_angle_4_deg 12.899 r_long_range_B_refined 6.378 r_long_range_B_other 6.369 r_dihedral_angle_1_deg 5.173 r_scangle_other 4.773 r_mcangle_it 3.646 r_mcangle_other 3.645 r_scbond_it 3.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.433 r_dihedral_angle_3_deg 16.921 r_dihedral_angle_4_deg 12.899 r_long_range_B_refined 6.378 r_long_range_B_other 6.369 r_dihedral_angle_1_deg 5.173 r_scangle_other 4.773 r_mcangle_it 3.646 r_mcangle_other 3.645 r_scbond_it 3.138 r_scbond_other 3.136 r_mcbond_it 2.401 r_mcbond_other 2.394 r_angle_refined_deg 1.689 r_angle_other_deg 0.889 r_chiral_restr 0.094 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1982 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement