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The ligand-free structure of human PPARgamma LBD R288H 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 2.72 54.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.396 α = 90 b = 51.997 β = 90 c = 54.052 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 2017-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9793 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 50 99.7 0.073 0.995 31.63 9.8 19382
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 2.2 2.24 100 0.646 0.92 4.31 10.1
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 2.2 36.041 19283 945 99.53 0.238 0.2369 0.2424 0.2636 0.2653 38.16
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] 0.259 0.132 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.78 r_dihedral_angle_4_deg 25.997 r_dihedral_angle_3_deg 14.829 r_lrange_it 8.101 r_lrange_other 8.1 r_dihedral_angle_1_deg 5.976 r_scangle_it 5.27 r_scangle_other 5.27 r_mcangle_it 4.967 r_mcangle_other 4.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.78 r_dihedral_angle_4_deg 25.997 r_dihedral_angle_3_deg 14.829 r_lrange_it 8.101 r_lrange_other 8.1 r_dihedral_angle_1_deg 5.976 r_scangle_it 5.27 r_scangle_other 5.27 r_mcangle_it 4.967 r_mcangle_other 4.967 r_scbond_other 3.137 r_scbond_it 3.135 r_mcbond_it 3.018 r_mcbond_other 3.013 r_angle_refined_deg 1.365 r_angle_other_deg 1.221 r_nbd_other 0.237 r_symmetry_nbd_refined 0.23 r_nbd_refined 0.212 r_symmetry_nbd_other 0.182 r_xyhbond_nbd_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.169 r_nbtor_refined 0.161 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2219 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing