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Vitamin D receptor complexed with a lithocholic 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 7 297 0.1 M MOPS-NaOH, 0.1-0.4 M sodium formate, 12-22% (w/v) PEG4000, 5% (v/v) ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.86 34.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.805 α = 90 b = 37.581 β = 98.59 c = 40.913 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 2021-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.94 40 98.4 0.056 0.999 8.6 3.4 17530
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.01 98.2 0.567 0.876 1.7 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ZLC 1.94 40 17523 848 98.058 0.209 0.207 0.2072 0.2424 0.2422 33.815
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] 0.109 -0.06 -0.11 0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.268 r_dihedral_angle_4_deg 16.235 r_dihedral_angle_3_deg 15.375 r_lrange_it 6.69 r_lrange_other 6.688 r_dihedral_angle_1_deg 5.581 r_scangle_it 5.176 r_scangle_other 5.174 r_mcangle_it 3.692 r_mcangle_other 3.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.268 r_dihedral_angle_4_deg 16.235 r_dihedral_angle_3_deg 15.375 r_lrange_it 6.69 r_lrange_other 6.688 r_dihedral_angle_1_deg 5.581 r_scangle_it 5.176 r_scangle_other 5.174 r_mcangle_it 3.692 r_mcangle_other 3.691 r_scbond_it 3.405 r_scbond_other 3.401 r_mcbond_it 2.564 r_mcbond_other 2.562 r_angle_refined_deg 1.514 r_angle_other_deg 1.306 r_symmetry_nbd_refined 0.209 r_nbd_refined 0.208 r_symmetry_nbd_other 0.165 r_nbd_other 0.162 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.112 r_chiral_restr 0.077 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1927 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing