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X-ray crystal structure of the nuclear hormone receptor PPAR-gamma in a complex with a compound with dual PPAR gamma agonism and Angiotensin II Type I receptor antagonism activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IA6 PDB entry 3IA6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 Apo crystals grown from Citrate/Imidazole, then soaked with 0.5 mM compound 2a, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.697 α = 90 b = 61.831 β = 102.04 c = 118.936 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 210 2004-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.41 37.8 95.67 0.033 24 3.3 24622 24537 1 1 66.2
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 2.41 2.52 95.6
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 PDB entry 3IA6 2.41 37.8 24622 24537 1287 95.67 0.2327 0.2327 0.2302 0.2335 0.2807 0.2953 RANDOM 74.54
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] 1.5178 -0.1325 0.295 -1.8128
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.7 t_omega_torsion 2.18 t_angle_deg 1.08 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3912 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 66
Software Software Software Name Purpose ADSC data collection REFMAC refinement BUSTER refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing