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The ligand-free structure of human PPARgamma LBD F287Y mutant in the presence of the SRC-1 coactivator peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 2.2 M sodium malonate (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.71 54.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.748 α = 90 b = 52.377 β = 90 c = 53.973 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 270 2017-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97934 PAL/PLS 5C (4A)
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 2.3 50 99.6 0.054 31.8 7.7 17093
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 100 0.66 3.06 7.8
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 5GTP 2.3 48.668 16498 831 96.221 0.245 0.2434 0.2488 0.2761 0.2799 41.091
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 -0.158 -0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.924 r_dihedral_angle_4_deg 18.822 r_dihedral_angle_3_deg 14.78 r_lrange_other 10.042 r_lrange_it 10.038 r_scangle_other 6.577 r_scangle_it 6.576 r_dihedral_angle_1_deg 6.201 r_mcangle_it 5.873 r_mcangle_other 5.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.924 r_dihedral_angle_4_deg 18.822 r_dihedral_angle_3_deg 14.78 r_lrange_other 10.042 r_lrange_it 10.038 r_scangle_other 6.577 r_scangle_it 6.576 r_dihedral_angle_1_deg 6.201 r_mcangle_it 5.873 r_mcangle_other 5.871 r_scbond_other 3.73 r_scbond_it 3.728 r_mcbond_other 3.607 r_mcbond_it 3.606 r_angle_refined_deg 1.306 r_angle_other_deg 1.208 r_symmetry_nbd_refined 0.345 r_nbd_other 0.329 r_symmetry_xyhbond_nbd_refined 0.25 r_nbd_refined 0.215 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.156 r_symmetry_xyhbond_nbd_other 0.126 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.06 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2197 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing