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X-ray structure of human PPARalpha ligand binding domain-stearic acid co-crystals obtained by delipidation and cross-seeding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 0.1 M Tris (pH 8.5), 25 %(w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.782 α = 90 b = 61.452 β = 106.52 c = 52.971 γ = 90
Symmetry Space Group P 1 21 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 Mirrors 2018-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.00000 Photon Factory BL-17A
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 1.41 42.93 98.3 0.039 0.046 0.025 0.999 17.5 3.5 52187 11.74
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 1.41 1.43 96.3 0.334 0.394 0.207 0.902 3.6 3.5
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 3VI8 1.41 26.289 1.91 52173 4981 95.91 0.1757 0.1748 0.174 0.1921 0.1926 15.8994
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 14.93 f_angle_d 1.061 f_chiral_restr 0.074 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2121 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 69
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction