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Crystal structure of Peroxisome proliferator-activated receptor gamma (PPARG)in complex with garcinoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TSG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 1.2 M ammonium sulfate, 0.1 M tris, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.64 53.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.369 α = 90 b = 65.369 β = 90 c = 156.545 γ = 90
Symmetry Space Group P 43 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 DECTRIS EIGER2 X 16M 2020-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9999 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.93 46.22 99.8 0.051 0.058 0.021 0.999 17.2 8.1 26357
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2 100 0.97 0.91 0.358 0.819 2.2 8.4
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 6TSG 1.93 46.22 24979 1321 99.7 0.1909 0.1887 0.1971 0.2302 0.2397 RANDOM 50.91
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] 0.93 0.93 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.987 r_dihedral_angle_4_deg 17.325 r_dihedral_angle_3_deg 13.407 r_dihedral_angle_1_deg 6.499 r_angle_refined_deg 1.389 r_angle_other_deg 1.364 r_chiral_restr 0.079 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.987 r_dihedral_angle_4_deg 17.325 r_dihedral_angle_3_deg 13.407 r_dihedral_angle_1_deg 6.499 r_angle_refined_deg 1.389 r_angle_other_deg 1.364 r_chiral_restr 0.079 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2172 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 93
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing