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crystal structure of VDR in complex with Des-C-Ring and Aromatic-D-Ring analog 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 LiSO4 1.6M, Hepes 0.1M pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.3 46.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.599 α = 90 b = 65.599 β = 90 c = 264.121 γ = 120
Symmetry Space Group P 65 2 2
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 EIGER X 9M 2022-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.98 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.3 47.74 98.81 1 19.28 20 15928 67.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.382 0.775
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 47.74 1.33 15810 995 99.21 0.2094 0.2056 0.212 0.2651 0.2693 92.69
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.7824 f_angle_d 0.8585 f_chiral_restr 0.0466 f_plane_restr 0.0076 f_bond_d 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1994 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing