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PPARgamma ligand-binding domain in complex with PG08
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 283 0.1 M KCl, 0.1 M MgCl2, 18% PEG Smear Medium, and 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.2 44.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.62 α = 90 b = 53.46 β = 105.901 c = 66.91 γ = 90
Symmetry Space Group P 1 21 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 9M 2023-12-04 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 1.44 41.99 99.9 0.998 10.9 21.8 53707
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 1.44 1.53 0.632
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8HUM 1.44 41.986 53689 2002 99.993 0.173 0.1717 0.1709 0.2013 0.2005 22.921
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] -0.283 0.104 0.597 -0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.978 r_dihedral_angle_3_deg 12.947 r_dihedral_angle_2_deg 7.563 r_lrange_it 6.218 r_lrange_other 6.128 r_dihedral_angle_1_deg 5.525 r_scangle_it 3.546 r_scangle_other 3.545 r_scbond_it 2.273 r_scbond_other 2.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.978 r_dihedral_angle_3_deg 12.947 r_dihedral_angle_2_deg 7.563 r_lrange_it 6.218 r_lrange_other 6.128 r_dihedral_angle_1_deg 5.525 r_scangle_it 3.546 r_scangle_other 3.545 r_scbond_it 2.273 r_scbond_other 2.272 r_mcangle_other 2.193 r_mcangle_it 2.192 r_angle_refined_deg 1.89 r_mcbond_it 1.336 r_mcbond_other 1.334 r_angle_other_deg 0.601 r_nbd_refined 0.242 r_symmetry_nbd_refined 0.212 r_nbd_other 0.194 r_symmetry_nbd_other 0.189 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.182 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.039 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_chiral_restr_other 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2214 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing