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Structure-based Design of Indole Propionic Acids as Novel PPARag CO-Agonists
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in house structure of PPARg
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M TRIS, PEG 3350, 0.2M MGSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.239 α = 90 b = 68.319 β = 90 c = 87.952 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 110 IMAGE PLATE MAR scanner 345 mm plate 2002-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR571 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 30 94 18856 18856
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.18 96
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT in house structure of PPARg 2.1 20 18856 17716 957 95.07 0.19848 0.19522 0.1959 0.26075 0.2617 RANDOM 29.397
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] -0.38 1.45 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.513 r_scangle_it 3.825 r_scbond_it 2.239 r_mcangle_it 1.401 r_angle_refined_deg 1.37 r_mcbond_it 0.718 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.168 r_symmetry_hbond_refined 0.119 r_symmetry_vdw_refined 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.513 r_scangle_it 3.825 r_scbond_it 2.239 r_mcangle_it 1.401 r_angle_refined_deg 1.37 r_mcbond_it 0.718 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.168 r_symmetry_hbond_refined 0.119 r_symmetry_vdw_refined 0.098 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2149 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement