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Crystal structure of PPAR gamma ligand binding domain in complex with a novel partial agonist GQ-16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FUR PDB ENTRY 3FUR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.2 M Ammonium acetate, 0.1 M Sodium citrate, pH 5.6, 30%(w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.48 50.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.69 α = 90 b = 84.39 β = 90 c = 96.98 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 95 CCD ADSC QUANTUM 210 2009-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0000 ALS 5.0.1
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 1.8 42.54 98 67318
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3FUR 2.1 42.044 1.34 39920 4017 97.96 0.2122 0.2084 0.2466 0.2542 RANDOM
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] -10.9077 20.2744 -7.9998
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.725 f_angle_d 1.317 f_chiral_restr 0.074 f_bond_d 0.01 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4249 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 50
Software Software Software Name Purpose ADSC data collection PHASER phasing PHENIX refinement MOSFLM data reduction SCALA data scaling