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Crystal structure of the complex between PPARgamma and the partial agonist LT127 (ureidofibrate derivative). This structure has been obtained from crystals soaked for 6 hours.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PRG PDB ENTRY 1PRG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.8 M NaCitrate, 0.15 M Tris.
Crystals of the apo-form have been soaked for 6 hours in a solution containing the ligand, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93 α = 90 b = 60.14 β = 103.7 c = 118.08 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 MARRESEARCH 2005-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.2 ELETTRA 5.2R
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 2.25 30 97.7 0.052 16.9 3.5 29712 29712 38.8
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) 2.25 2.33 94.7 0.408 2.9 3.5 2862
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS PDB ENTRY 1PRG 2.25 8 2 28944 28691 1410 96.8 0.238 0.2434 0.29 0.2959 random 47.712
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] 4.562 -2.096 -14.104 9.542
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.25 c_mcangle_it 2.298 c_scbond_it 2.196 c_mcbond_it 1.428 c_angle_deg 1.186 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4406 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 33
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction MAR345 data collection CNS phasing