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Human PPAR gamma ligand binding domain in complex with a synthetic agonist TIPP703
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KNU pdb entry 1KNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.8M Sodium citrate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.307 α = 90 b = 61.604 β = 103.64 c = 118.973 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 RIGAKU JUPITER 210 2007-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 2.4 50 97.1 0.041 15.3 3.5 25166 33.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 80.3 0.261 2.8 2065
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1KNU 2.4 49.09 24151 1160 93.1 0.24 0.24 0.2382 0.286 0.2842 RANDOM 49.5
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] -4.13 4.38 17.03 -12.91
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.2 c_scangle_it 2.61 c_mcangle_it 1.98 c_scbond_it 1.69 c_angle_deg 1.3 c_mcbond_it 1.19 c_improper_angle_d 0.8 c_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4110 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 66
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing