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Human PPAR-gamma ligand binding domain in complex with AKGO166
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q5P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.9M-1.2M sodium citrate tribasic dihydrate, 0.1M sodium cacodylate pH 6.4-7.4
Crystal Properties Matthews coefficient Solvent content 2.68 54.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.335 α = 90 b = 61.203 β = 101.64 c = 119.062 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 PIXEL DECTRIS EIGER X 4M 2024-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967697 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 27.94 100 0.996 7.1 7.5 39036
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 0.721
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 27.94 37059 1974 99.94 0.22421 0.22272 0.2302 0.25118 0.2567 RANDOM 46.616
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] 2.78 1.86 0.73 -3.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.94 r_dihedral_angle_3_deg 13.627 r_long_range_B_refined 7.272 r_long_range_B_other 7.272 r_dihedral_angle_1_deg 6.084 r_scangle_other 5.656 r_mcangle_other 5.05 r_mcangle_it 5.045 r_scbond_it 3.842 r_scbond_other 3.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.94 r_dihedral_angle_3_deg 13.627 r_long_range_B_refined 7.272 r_long_range_B_other 7.272 r_dihedral_angle_1_deg 6.084 r_scangle_other 5.656 r_mcangle_other 5.05 r_mcangle_it 5.045 r_scbond_it 3.842 r_scbond_other 3.842 r_mcbond_it 3.47 r_mcbond_other 3.459 r_angle_refined_deg 1.45 r_angle_other_deg 0.498 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4040 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing Coot model building