☰ Navigation Tabs
Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having an ene-ynone 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 2.13 42.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.3 α = 90 b = 42.52 β = 95.72 c = 41.96 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 PILATUS 2M 2016-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.00 Photon Factory AR-NE3A
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 2.38 32.7 96.2 8.7 2.8 10580
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 2.38 2.47
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.38 32.7 10001 522 94.87 0.23689 0.23463 0.27889 0.292 RANDOM 40.61
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] -4.5 -1.36 4.79 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.376 r_dihedral_angle_3_deg 16.137 r_dihedral_angle_4_deg 8.756 r_long_range_B_refined 5.657 r_long_range_B_other 5.657 r_dihedral_angle_1_deg 5.006 r_mcangle_it 3.619 r_mcangle_other 3.618 r_scangle_other 3.58 r_mcbond_it 2.465
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.376 r_dihedral_angle_3_deg 16.137 r_dihedral_angle_4_deg 8.756 r_long_range_B_refined 5.657 r_long_range_B_other 5.657 r_dihedral_angle_1_deg 5.006 r_mcangle_it 3.619 r_mcangle_other 3.618 r_scangle_other 3.58 r_mcbond_it 2.465 r_mcbond_other 2.459 r_scbond_it 2.418 r_scbond_other 2.417 r_angle_refined_deg 1.616 r_angle_other_deg 1.309 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_other 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.007 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 1927 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing