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X-ray structure of human PPARalpha ligand binding domain-GW7647 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 0.1M Tris (pH 8.5), 25%(w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.804 α = 90 b = 62.016 β = 106.5 c = 53.076 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 2019-02-23 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 1.45 42.96 98 0.027 0.032 0.017 1 21.1 3.4 48395 16.17
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 1.45 1.47 96.9 0.329 0.389 0.205 0.9 3.5 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 1.45 39.34 1.95 48387 4598 95.76 0.1882 0.1871 0.188 0.208 0.2112 21.6423
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 2058 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 41
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement