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Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having a vinyl ketone group via conjugate addition reaction
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
Crystal Properties Matthews coefficient Solvent content 2.11 41.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.53 α = 90 b = 42.44 β = 95.98 c = 41.87 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 CCD ADSC QUANTUM 315r 2015-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00 Photon Factory BL-5A
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 2.72 41.64 94.7 88.8 3.6 7161
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 2.72 2.86
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 THROUGHOUT 2.72 41.64 6463 693 96.94 0.22839 0.22585 0.2312 0.2519 0.2486 RANDOM 40.228
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] -3.9 -1.43 5.63 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.341 r_dihedral_angle_4_deg 20.876 r_dihedral_angle_3_deg 17.874 r_long_range_B_refined 4.433 r_long_range_B_other 4.429 r_dihedral_angle_1_deg 4.089 r_angle_other_deg 3.975 r_mcangle_it 2.507 r_mcangle_other 2.507 r_scangle_other 2.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.341 r_dihedral_angle_4_deg 20.876 r_dihedral_angle_3_deg 17.874 r_long_range_B_refined 4.433 r_long_range_B_other 4.429 r_dihedral_angle_1_deg 4.089 r_angle_other_deg 3.975 r_mcangle_it 2.507 r_mcangle_other 2.507 r_scangle_other 2.441 r_scbond_it 1.558 r_scbond_other 1.558 r_mcbond_it 1.555 r_mcbond_other 1.546 r_angle_refined_deg 1.221 r_chiral_restr 0.071 r_gen_planes_other 0.03 r_bond_refined_d 0.027 r_gen_planes_refined 0.011 r_bond_other_d 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 1981 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing