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X-ray structure of human PPARalpha ligand binding domain-5,8,11,14-eicosatetraynoic acid (ETYA) co-crystals obtained by soaking
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 Bis-Tris(pH 6.5), 25 %(w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.736 α = 90 b = 61.725 β = 106.47 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 4M Mirrors 2017-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.00000 SPring-8 BL26B1
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 1.35 42.9 96.7 0.019 0.023 0.012 1 30.8 3.6 58620 12.77
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 1.35 1.37 94.6 0.148 0.174 0.09 0.984 7.4 3.7
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 1.35 39.223 1.92 58543 5528 95.21 0.1811 0.1803 0.1844 0.1951 0.1988 18.4855
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2090 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 28
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement