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Structure of PPARalpha with 3-[5-Methoxy-1-(4-methoxy-benzenesulfonyl)-1H-indol-3-yl]-propionic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KKQ PDB entry 1KKQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 277 The purified PPARa LBD protein was diluted to 10 mg/ml and 1mM of indeglitazar and 2x molar excess of SRC-1 peptide were added prior to crystallization by mixing equal volumes of protein/compound sample with reservoir solution containing 16% PEG 8000, 0.1 M Tris buffer at pH 8.0, 0.02 M lithium sulfate, and 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.73 54.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.869 α = 90 b = 89.595 β = 90 c = 101.115 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 210 2005-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.5 50 99.8 0.045 4.8 26993
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.57 99.5 0.319 1.3 4.9
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB entry 1KKQ 2.5 44.8 1.35 27007 26918 1352 99.7 0.198 0.195 0.2086 0.258 0.2715
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] -15.915 5.8565 10.0586
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.63 f_angle_d 0.95 f_chiral_restr 0.06 f_bond_d f_plane_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4499 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 54
Software Software Software Name Purpose Blu-Ice data collection CCP4 model building PHENIX refinement MOSFLM data reduction SCALA data scaling CCP4 phasing