☰ Navigation Tabs
Crystal structure of PPARgamma ligand binding domain (LBD) in complex with NCoR1 corepressor peptide and inverse agonist FX-909
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ONI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M MES (pH 6.5), 0.2 M Ammonium Sulfate, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.043 α = 90 b = 62.043 β = 90 c = 166.259 γ = 90
Symmetry Space Group P 41 21 2
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 Bruker PHOTON III 2024-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE Excillum MetalJet D2+ 160 kV 1.342
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 20.89 77.54 0.291 4.68 7.1 18172 18.42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.175 63.2 0.9047 0.407 1.03 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 20.89 0.02 15357 1539 77.66 0.2449 0.2391 0.2394 0.2975 0.2978 22.96
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.0719 f_angle_d 1.0391 f_chiral_restr 0.0515 f_bond_d 0.0082 f_plane_restr 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2188 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 21
Software Software Software Name Purpose PROTEUM PLUS data collection PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing PHENIX refinement