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X-ray Crystal structure of the nuclear hormone receptor PPAR-gamma in a complex with a PPAR gamma/alpha dual agonist
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CRK PDB Entry 2CRK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 mM Immidizole, 860 mM Sodium Citrate, Glycerol 5 % (v/v) , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.71 54.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.455 α = 90 b = 62.016 β = 102.54 c = 118.66 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 ADSC QUANTUM 210 2004-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
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 35 89.8 0.056 26 3.5 29706 28675 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.33 52.8 0.375 1.8 2.1 3509
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 2CRK 2.3 35 1 1 29706 26150 1420 92.81 0.2254 0.22239 0.2171 0.28223 0.2723 RANDOM 74.217
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] -2.53 -1.76 7.23 -5.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.658 r_dihedral_angle_3_deg 17.038 r_dihedral_angle_4_deg 15.345 r_dihedral_angle_1_deg 5.203 r_scangle_it 1.359 r_angle_refined_deg 1.143 r_angle_other_deg 1.124 r_scbond_it 0.882 r_mcangle_it 0.69 r_mcbond_it 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.658 r_dihedral_angle_3_deg 17.038 r_dihedral_angle_4_deg 15.345 r_dihedral_angle_1_deg 5.203 r_scangle_it 1.359 r_angle_refined_deg 1.143 r_angle_other_deg 1.124 r_scbond_it 0.882 r_mcangle_it 0.69 r_mcbond_it 0.61 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.201 r_symmetry_vdw_other 0.181 r_nbtor_refined 0.178 r_nbd_other 0.16 r_xyhbond_nbd_refined 0.12 r_nbtor_other 0.086 r_mcbond_other 0.069 r_chiral_restr 0.06 r_symmetry_hbond_refined 0.039 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4046 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing