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Vitamin D receptor complex with a dimethylbis((3-trifluoromethyl)phenyl)silane 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, SITTING DROP 293 0.2 M magnesium acetate tetrahydrate, PEG 3350, pH 7.9.
Crystal Properties Matthews coefficient Solvent content 1.93 36.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.16 α = 90 b = 43.01 β = 93.314 c = 45.59 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 EIGER X 16M 2024-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0 SPring-8 BL45XU
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 2.02 45.52 99.6 0.154 0.998 9.62 8 16309
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.14 2.996 0.516
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2ZLC 2.02 45.51 1.34 16262 816 99.3 0.1856 0.1838 0.1864 0.2215 0.224 54.97
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 24.3175 f_angle_d 0.6372 f_chiral_restr 0.0374 f_bond_d 0.0048 f_plane_restr 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2015 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing