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Human PPAR-gamma ligand binding domain in complex with LW76
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 2.8 56.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.137 α = 90 b = 60.973 β = 101.56 c = 119.269 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 27.64 100 0.996 6.9 7.5 38475
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 0.569
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 27.64 36526 1949 99.94 0.2116 0.20957 0.215 0.24839 0.2501 RANDOM 48.104
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] 0.95 1 1.68 -2.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.71 r_dihedral_angle_3_deg 12.48 r_long_range_B_other 8.327 r_long_range_B_refined 8.326 r_scangle_other 6.632 r_dihedral_angle_1_deg 5.807 r_mcangle_it 5.591 r_mcangle_other 5.59 r_scbond_it 4.348 r_scbond_other 4.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.71 r_dihedral_angle_3_deg 12.48 r_long_range_B_other 8.327 r_long_range_B_refined 8.326 r_scangle_other 6.632 r_dihedral_angle_1_deg 5.807 r_mcangle_it 5.591 r_mcangle_other 5.59 r_scbond_it 4.348 r_scbond_other 4.347 r_mcbond_it 3.868 r_mcbond_other 3.868 r_angle_refined_deg 1.364 r_angle_other_deg 0.486 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 4011 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing Coot model building PDB-REDO refinement