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Crystal structure of VDR-LBD complexed with an antagonist, 2-methylidene-19,26,27-trinor-22-(S)-butyl-1-hydroxy-25-oxo-25-(1H-pyrrol-2-yl)- vitamin 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 2.04 39.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.8 α = 90 b = 41.49 β = 96.97 c = 42.02 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 1.0 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 2.8 41.71 99 9.6 3.3 6482
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 2.8 41.71 6021 460 98.59 0.18393 0.18296 0.1893 0.19649 0.204 RANDOM 30.861
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] -3.44 -0.46 2.32 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.892 r_dihedral_angle_3_deg 17.621 r_dihedral_angle_4_deg 16.533 r_dihedral_angle_1_deg 5.285 r_long_range_B_other 4.787 r_long_range_B_refined 4.783 r_angle_other_deg 3.525 r_scangle_other 3.188 r_mcangle_it 2.743 r_mcangle_other 2.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.892 r_dihedral_angle_3_deg 17.621 r_dihedral_angle_4_deg 16.533 r_dihedral_angle_1_deg 5.285 r_long_range_B_other 4.787 r_long_range_B_refined 4.783 r_angle_other_deg 3.525 r_scangle_other 3.188 r_mcangle_it 2.743 r_mcangle_other 2.743 r_scbond_it 1.954 r_scbond_other 1.954 r_mcbond_it 1.607 r_mcbond_other 1.605 r_angle_refined_deg 1.437 r_chiral_restr 0.063 r_bond_refined_d 0.01 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 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 1891 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling REFMAC phasing