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PPARgamma Ligand binding domain complexed with a farglitazar analogue gw4709
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other PPARgamma lbd
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 100mM Hepes and 1.4M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.68 54.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.916 α = 90 b = 62.006 β = 101.94 c = 118.172 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 2000-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 24.5 91.1 0.052 0.052 22.97 4.5 29454 26825 -3 -3 49.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 65.3 0.483 0.483 1.61 2.4 2940
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 PPARgamma lbd 2.3 24.5 25923 875 90.99 0.22612 0.2245 0.2792 0.27302 0.3238 RANDOM 59.851
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] -0.33 -0.39 -0.35 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.04 r_dihedral_angle_4_deg 21.435 r_dihedral_angle_3_deg 16.844 r_dihedral_angle_1_deg 6.227 r_scangle_it 2.179 r_scbond_it 1.483 r_angle_refined_deg 1.265 r_mcangle_it 0.939 r_angle_other_deg 0.9 r_mcbond_it 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.04 r_dihedral_angle_4_deg 21.435 r_dihedral_angle_3_deg 16.844 r_dihedral_angle_1_deg 6.227 r_scangle_it 2.179 r_scbond_it 1.483 r_angle_refined_deg 1.265 r_mcangle_it 0.939 r_angle_other_deg 0.9 r_mcbond_it 0.58 r_symmetry_hbond_refined 0.234 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.199 r_nbd_other 0.183 r_symmetry_vdw_other 0.183 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.157 r_mcbond_other 0.11 r_nbtor_other 0.087 r_chiral_restr 0.066 r_xyhbond_nbd_other 0.03 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other 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 3962 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing