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Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,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, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.286 α = 90 b = 43.851 β = 96.18 c = 42.321 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 4 2009-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.97800 Photon Factory BL-6A
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 2.1 50 99.3 16456
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 2.1 38.61 15502 827 99.24 0.23408 0.2319 0.2306 0.2749 0.2763 RANDOM 88.341
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] -3.03 -1 5.57 -2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.53 r_dihedral_angle_4_deg 21.76 r_dihedral_angle_3_deg 18.998 r_dihedral_angle_1_deg 5.004 r_angle_other_deg 3.582 r_angle_refined_deg 1.765 r_chiral_restr 0.091 r_gen_planes_other 0.017 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.53 r_dihedral_angle_4_deg 21.76 r_dihedral_angle_3_deg 18.998 r_dihedral_angle_1_deg 5.004 r_angle_other_deg 3.582 r_angle_refined_deg 1.765 r_chiral_restr 0.091 r_gen_planes_other 0.017 r_bond_refined_d 0.016 r_gen_planes_refined 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1997 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 34
Software Software Software Name Purpose SERGUI data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling