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Crystal structure of VDR-LBD/partial agonist complex: 22S-ethyl analogue
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 2.09 41.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.03 α = 90 b = 41.97 β = 95.96 c = 41.86 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 2014-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 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 2.9 40.48 75.2 56 2 9246
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 2.9 40.48 4318 207 74.2 0.21074 0.20817 0.2123 0.26653 0.2657 RANDOM 87.392
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] -6.08 -1.28 6.24 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.795 r_dihedral_angle_3_deg 16.584 r_dihedral_angle_4_deg 11.484 r_long_range_B_refined 7.314 r_long_range_B_other 7.312 r_scangle_other 4.686 r_mcangle_it 4.61 r_mcangle_other 4.608 r_dihedral_angle_1_deg 3.937 r_angle_other_deg 3.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.795 r_dihedral_angle_3_deg 16.584 r_dihedral_angle_4_deg 11.484 r_long_range_B_refined 7.314 r_long_range_B_other 7.312 r_scangle_other 4.686 r_mcangle_it 4.61 r_mcangle_other 4.608 r_dihedral_angle_1_deg 3.937 r_angle_other_deg 3.471 r_scbond_it 2.769 r_scbond_other 2.768 r_mcbond_it 2.715 r_mcbond_other 2.715 r_angle_refined_deg 1.128 r_chiral_restr 0.053 r_gen_planes_other 0.021 r_gen_planes_refined 0.011 r_bond_refined_d 0.009 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 2004 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement iMOSFLM data scaling