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A novel anti-adipogenic partial agonist of peroxisome proliferator-activated receptor-gamma (PPARG) recruits pparg-coactivator-1 alpha (PGC1A) but potentiates insulin signaling in vitro
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other IN HOUSE PPARG STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 20% PEG3350, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.483 α = 90 b = 65.897 β = 90 c = 87.538 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 100 CCD MARRESEARCH 2004-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.7997 SLS X06SA
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 1.99 30 99.6 21716 21716
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 97.4
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 (All) 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 PPARG STRUCTURE 1.99 30 21575 21575 1105 99.6 0.19225 0.19225 0.18942 0.1878 0.24586 0.2452 RANDOM 35.317
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] -0.11 1.84 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.59 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_3_deg 16.511 r_dihedral_angle_1_deg 5.444 r_scangle_it 4.18 r_scbond_it 2.709 r_mcangle_it 1.78 r_angle_refined_deg 1.582 r_mcbond_it 1.096 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.59 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_3_deg 16.511 r_dihedral_angle_1_deg 5.444 r_scangle_it 4.18 r_scbond_it 2.709 r_mcangle_it 1.78 r_angle_refined_deg 1.582 r_mcbond_it 1.096 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.29 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.125 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2149 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling