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Crystal Structure of Human PPAR-gamma Ligand Binding Domain Complexed with a Potent and Selective Agonist
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HWR PDB ENTRY 2HWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 28.25% PEG 3350. 0.016M sodium citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.36 47.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.502 α = 90 b = 88.892 β = 91.06 c = 58.371 γ = 90
Symmetry Space Group P 1 21 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 315 2007-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
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 2.3 30 99 0.082 15.07 25.02 25665
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) 2.3 2.39 100 0.382 5.08 2.4 2521
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 2HWR 2.3 26.12 23971 1279 97.97 0.23399 0.23049 0.2289 0.29785 0.2945 RANDOM 43.154
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] -0.55 -0.79 0.63 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.554 r_dihedral_angle_4_deg 24.168 r_dihedral_angle_3_deg 19.355 r_dihedral_angle_1_deg 7.423 r_scangle_it 4.709 r_scbond_it 2.491 r_mcangle_it 1.977 r_angle_refined_deg 1.866 r_mcbond_it 1.064 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.554 r_dihedral_angle_4_deg 24.168 r_dihedral_angle_3_deg 19.355 r_dihedral_angle_1_deg 7.423 r_scangle_it 4.709 r_scbond_it 2.491 r_mcangle_it 1.977 r_angle_refined_deg 1.866 r_mcbond_it 1.064 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.27 r_nbd_refined 0.234 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.137 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4356 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 44
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling