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X-ray structure of human PPARalpha ligand binding domain-GW9662-clofibric acid co-crystals obtained by delipidation and co-crystallization
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 3.05 59.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.71 α = 90 b = 102.478 β = 100.15 c = 61.465 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 PILATUS3 S 6M Mirrors 2018-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A
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 2.86 46.84 99.6 0.065 0.091 0.063 0.997 11.7 3.4 17144
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 2.86 3.01 99.5 0.314 0.439 0.306 0.885 3.2 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3VI8 2.86 36.615 1.93 17130 1636 97.41 0.1979 0.1954 0.2442 0.2128
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 4269 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 122
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement