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Crystal structure of VDR-LBD complexed with 2-methylidene-26,27-diphenyl-19-nor-1,25-dihydroxyvitamin 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 2.07 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.06 α = 90 b = 41.49 β = 97.44 c = 83.89 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 210 2014-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 30.14 85.9 10.7 2.8 30998
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 2.05
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 30.14 29468 1529 85.97 0.18251 0.17999 0.1887 0.22991 0.2381 RANDOM 24.549
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] -1.61 -0.55 1.61 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.705 r_dihedral_angle_4_deg 19.397 r_dihedral_angle_3_deg 16.793 r_long_range_B_refined 6.426 r_long_range_B_other 6.396 r_dihedral_angle_1_deg 5.173 r_scangle_other 4.217 r_mcangle_it 3.288 r_mcangle_other 3.288 r_scbond_it 2.646
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.705 r_dihedral_angle_4_deg 19.397 r_dihedral_angle_3_deg 16.793 r_long_range_B_refined 6.426 r_long_range_B_other 6.396 r_dihedral_angle_1_deg 5.173 r_scangle_other 4.217 r_mcangle_it 3.288 r_mcangle_other 3.288 r_scbond_it 2.646 r_scbond_other 2.645 r_mcbond_it 2.089 r_mcbond_other 2.089 r_angle_refined_deg 1.647 r_angle_other_deg 0.861 r_chiral_restr 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 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 4080 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement