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PPARgamma ligand-binding domain in complex with PG14
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HUM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M Bis-Tris HCl (pH 6.2 to 6.5), 23% PEG 3,350, and 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.19 43.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.51 α = 90 b = 85.14 β = 90 c = 99.67 γ = 90
Symmetry Space Group P 2 21 21
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 9M 2024-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU
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 1.75 43.01 100 0.999 23.6 84.6 28845
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 1.75 1.86 0.926 1.8
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 8HUM 1.75 43.05 27134 1629 99.88 0.19375 0.19158 0.2058 0.23042 0.2368 RANDOM 37.387
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] 4.23 -2.32 -1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.512 r_dihedral_angle_2_deg 9.118 r_long_range_B_refined 6.97 r_long_range_B_other 6.94 r_dihedral_angle_1_deg 5.799 r_scangle_other 4.435 r_mcangle_it 3 r_mcangle_other 2.999 r_scbond_other 2.758 r_scbond_it 2.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.512 r_dihedral_angle_2_deg 9.118 r_long_range_B_refined 6.97 r_long_range_B_other 6.94 r_dihedral_angle_1_deg 5.799 r_scangle_other 4.435 r_mcangle_it 3 r_mcangle_other 2.999 r_scbond_other 2.758 r_scbond_it 2.757 r_mcbond_it 1.944 r_mcbond_other 1.943 r_angle_refined_deg 1.673 r_angle_other_deg 0.617 r_chiral_restr 0.096 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 2220 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PARROT phasing