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Vitamin D receptor complex with a 3-{4-(m-carboran-1-yl)phenoxy}propanoic acid derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.03M citric acid, 0.07M BIS-TRIS propane pH 7.6, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.09 41.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.483 α = 90 b = 41.583 β = 96.487 c = 42.188 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 PIXEL DECTRIS PILATUS 6M 2025-05-15 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) R Merge I (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 1.93 41.92 99.7 0.086 0.997 14.2 3.4 20219 23.18
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 1.93 1.98 0.708 1.9
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 1.93 38.37 1.34 20207 1010 99.57 0.1777 0.1765 0.1766 0.2006 0.2012 27.25
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 15.989 f_angle_d 0.6082 f_chiral_restr 0.0348 f_plane_restr 0.0039 f_bond_d 0.0033
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1992 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing