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Crystal structure of human PPAR-gamma ligand binding domain complex with a potency improved 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 27.5% PEG 3350, 16mM sodium citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.26 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.404 α = 90 b = 87.744 β = 90.73 c = 57.674 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 2009-11-26 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 1.98 30 97.6 0.055 16.55 24.58 38549
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 1.98 2.05 97.9 0.368 3.17 3.2 3746
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 1.98 30 35717 1872 97.51 0.23298 0.23076 0.2311 0.27482 0.2727 RANDOM 30.981
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] 1.34 1.91 -0.89 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.935 r_dihedral_angle_4_deg 21.36 r_dihedral_angle_3_deg 14.142 r_scangle_it 6.118 r_dihedral_angle_1_deg 5.896 r_mcangle_it 5.59 r_scbond_it 3.934 r_mcbond_it 3.373 r_angle_refined_deg 1.378 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.935 r_dihedral_angle_4_deg 21.36 r_dihedral_angle_3_deg 14.142 r_scangle_it 6.118 r_dihedral_angle_1_deg 5.896 r_mcangle_it 5.59 r_scbond_it 3.934 r_mcbond_it 3.373 r_angle_refined_deg 1.378 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4356 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 82
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling