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Human PPAR-gamma ligand binding domain in complex with LW99
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 = 93.597 α = 90 b = 61.265 β = 101.984 c = 119.82 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 EIGER2 X 9M 2024-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873128 ESRF ID23-2
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 58.67 99.5 0.998 8.7 7 44814
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 2.05 0.616
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 58.67 42589 2192 99.36 0.21335 0.21164 0.2201 0.24729 0.2494 RANDOM 49.977
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] 0.46 -0.07 0.25 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.956 r_dihedral_angle_3_deg 15.145 r_dihedral_angle_1_deg 6.244 r_long_range_B_refined 4.837 r_long_range_B_other 4.823 r_scangle_other 2.211 r_mcangle_other 1.88 r_mcangle_it 1.879 r_scbond_it 1.294 r_scbond_other 1.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.956 r_dihedral_angle_3_deg 15.145 r_dihedral_angle_1_deg 6.244 r_long_range_B_refined 4.837 r_long_range_B_other 4.823 r_scangle_other 2.211 r_mcangle_other 1.88 r_mcangle_it 1.879 r_scbond_it 1.294 r_scbond_other 1.294 r_angle_refined_deg 1.271 r_mcbond_it 1.1 r_mcbond_other 1.099 r_angle_other_deg 0.466 r_chiral_restr 0.055 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4187 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing PDB-REDO refinement Coot model building