☰ Navigation Tabs
Structure of PPARdelta 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 1GWX PDB entry 1GWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 277 The purified PPARd LBD protein was diluted to 10mg/ml and 1mM of indeglitazar was added to the diluted protein prior to crystallization by mixing equal volumes of protein/compound sample with reservoir solution containing 16% PEG 3350, 0.1 M Tris buffer at pH 7.5, 0.2 M magnesium chloride, and 1% n-butanol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.71 54.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.402 α = 90 b = 94.353 β = 98.27 c = 97.183 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 93 CCD ADSC QUANTUM 210 2006-05-04 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 2.24 50 98.8 0.098 3.3 33526
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) 2.24 2.3 0.489 1 3.3 4927
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 1GWX 2.24 38.99 1.35 33911 33474 1689 98.7 0.188 0.185 0.242 0.2239
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] -0.7778 2.334 7.1072 -8.8198
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.82 f_angle_d 1.08 f_chiral_restr 0.06 f_bond_d f_plane_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4287 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 69
Software Software Software Name Purpose Blu-Ice data collection CCP4 model building PHENIX refinement MOSFLM data reduction SCALA data scaling CCP4 phasing