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Crystal structure of Linafexor-FXR complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DCT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.2 M Sodium malonate pH 7.0, 20% Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.27 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.478 α = 90 b = 67.455 β = 90 c = 58.304 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 S 6M 2020-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1.0 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.64 50 98.7 0.067 0.071 0.021 1 8.3 11.7 7697
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.64 2.69 93.6 0.925 0.981 0.314 0.746 8.9
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 2.8 46.23 1.37 6513 643 99.6 0.2699 0.2673 0.2629 0.2929 0.2911
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 19.741 f_angle_d 0.61 f_chiral_restr 0.036 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1868 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing