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Structure of PPARgamma 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 2PRG PDB entry 2PRG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 277 The purified PPARg LBD protein was diluted to 12 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 27% polyethylene glycol (PEG) 4000, 0.1 M 2-(bis-(2-hydroxy-ethyl)-amino)-2-hydroxymethyl- propane-1,3-diol (BisTris) buffer at pH 6.5, 0.2 M ammonium acetate, and 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.98 37.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.853 α = 90 b = 86.671 β = 90 c = 122.135 γ = 90
Symmetry Space Group C 2 2 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 2003-05-11 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 1.95 61.1 97.8 0.051 4.5 22003
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) 1.95 2 99.2 0.288 1.8 4.7
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 2PRG 1.95 61.07 1.34 20842 20354 1065 97.7 0.182 0.179 0.199 0.236 0.2505
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] -1.2466 9.1063 -7.8597
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.033 f_angle_d 0.924 f_chiral_restr 0.065 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2223 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 27
Software Software Software Name Purpose Blu-Ice data collection CCP4 model building PHENIX refinement MOSFLM data reduction SCALA data scaling CCP4 phasing