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Crystal structure of VDR-LBD complexed with 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, Ethyleneglycol
Crystal Properties Matthews coefficient Solvent content 2.17 43.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.56 α = 90 b = 43.39 β = 95.48 c = 42.13 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 2016-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 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 2.28 41.74 95.9 7.7 1.9 11584
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 2.28 41.74 11584 591 94.94 0.21572 0.21265 0.2168 0.27478 0.2703 RANDOM 36.061
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] -2.88 -0.49 3.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.834 r_dihedral_angle_4_deg 19.258 r_dihedral_angle_3_deg 17.823 r_long_range_B_refined 6.1 r_long_range_B_other 6.099 r_dihedral_angle_1_deg 4.935 r_scangle_other 4.328 r_mcangle_it 3.935 r_mcangle_other 3.934 r_scbond_it 2.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.834 r_dihedral_angle_4_deg 19.258 r_dihedral_angle_3_deg 17.823 r_long_range_B_refined 6.1 r_long_range_B_other 6.099 r_dihedral_angle_1_deg 4.935 r_scangle_other 4.328 r_mcangle_it 3.935 r_mcangle_other 3.934 r_scbond_it 2.776 r_scbond_other 2.776 r_mcbond_it 2.629 r_mcbond_other 2.627 r_angle_refined_deg 1.583 r_angle_other_deg 0.832 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1974 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement