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The X-ray Crystal Structure of PPAR-gamma in Complex with an Indole Derivative Modulator, GSK538, and an SRC-1 Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FM9 RCSB ENTRY 1fm9 chain D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 Diffraction grade crystals grew in 7-14 days at 22C using 2uL vapor diffused hanging drops made with 1uL of the complex and 1uL of the well solution comprised of 14% PEG4K, 0.2M NaSCN and 0.1M Bis-tris pH 6.5., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.49 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.335 α = 90 b = 84.158 β = 90 c = 96.425 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 ADSC QUANTUM 210 2006-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 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 2.1 50 99.6 0.038 45.7 7.2 40155 39982 -3
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 2.1 2.18 96.8 0.427 3.3 6.5
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 RCSB ENTRY 1fm9 chain D 2.1 41.85 38828 1247 99.53 0.19915 0.19812 0.1986 0.23014 0.2308 RANDOM 40.254
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] 0.01 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.952 r_dihedral_angle_4_deg 17.365 r_dihedral_angle_3_deg 13.985 r_dihedral_angle_1_deg 6.002 r_scangle_it 2.32 r_scbond_it 1.425 r_angle_refined_deg 1.256 r_mcangle_it 0.922 r_angle_other_deg 0.887 r_mcbond_it 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.952 r_dihedral_angle_4_deg 17.365 r_dihedral_angle_3_deg 13.985 r_dihedral_angle_1_deg 6.002 r_scangle_it 2.32 r_scbond_it 1.425 r_angle_refined_deg 1.256 r_mcangle_it 0.922 r_angle_other_deg 0.887 r_mcbond_it 0.49 r_mcbond_other 0.09 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4239 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 78
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction JDirector data collection MOLREP phasing