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Crystal structure of PPARg ligand-binding domain in complex with NCoR1 peptide and FTX-6746
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, HANGING DROP 291 0.1 M MES pH 6.5, 0.1M Ammonium Sulfate, 24% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.33 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.13 α = 101.193 b = 70.33 β = 106.579 c = 92.68 γ = 104.98
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 2021-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12713 APS 21-ID-D
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 2.83 48.046 90 0.995 5.1 3.7 25524
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 2.83 2.98 0.889
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.83 48.046 24151 1159 85.183 0.234 0.2309 0.2349 0.2983 0.299 86.128
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] -3.222 2.106 -1.876 9.688 0.423 -5.469
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.438 r_lrange_it 14.68 r_lrange_other 14.679 r_dihedral_angle_6_deg 14.56 r_scangle_it 10.895 r_scangle_other 10.894 r_mcangle_it 10.59 r_mcangle_other 10.59 r_mcbond_it 6.891 r_mcbond_other 6.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.438 r_lrange_it 14.68 r_lrange_other 14.679 r_dihedral_angle_6_deg 14.56 r_scangle_it 10.895 r_scangle_other 10.894 r_mcangle_it 10.59 r_mcangle_other 10.59 r_mcbond_it 6.891 r_mcbond_other 6.89 r_scbond_it 6.808 r_scbond_other 6.808 r_dihedral_angle_1_deg 5.695 r_dihedral_angle_other_3_deg 5.286 r_dihedral_angle_2_deg 4.8 r_angle_refined_deg 1.355 r_angle_other_deg 0.462 r_nbd_refined 0.229 r_nbd_other 0.213 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.185 r_symmetry_nbd_refined 0.173 r_xyhbond_nbd_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.144 r_ncsr_local_group_3 0.104 r_ncsr_local_group_5 0.102 r_ncsr_local_group_6 0.102 r_ncsr_local_group_8 0.1 r_ncsr_local_group_9 0.095 r_ncsr_local_group_2 0.092 r_ncsr_local_group_7 0.092 r_ncsr_local_group_4 0.086 r_ncsr_local_group_1 0.078 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.061 r_chiral_restr_other 0.032 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7842 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing