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The ligand-free structure of human PPARgamma LBD C285Y 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 2.68 54.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.73 α = 90 b = 51.936 β = 90 c = 54.133 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) 0.97940 PAL/PLS 5C (4A)
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 2.35 50 99 0.053 1 28.21 5.7 16225
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 2.35 2.39 97.9 0.584 0.874 2.64 5.8
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 2.35 48.313 14927 758 93.375 0.231 0.2292 0.2333 0.2693 0.2733 38.006
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] 0.138 -0.048 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.711 r_dihedral_angle_4_deg 15.32 r_dihedral_angle_3_deg 15.211 r_lrange_it 8.724 r_lrange_other 8.714 r_dihedral_angle_1_deg 5.923 r_scangle_it 5.428 r_scangle_other 5.424 r_mcangle_it 5.06 r_mcangle_other 5.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.711 r_dihedral_angle_4_deg 15.32 r_dihedral_angle_3_deg 15.211 r_lrange_it 8.724 r_lrange_other 8.714 r_dihedral_angle_1_deg 5.923 r_scangle_it 5.428 r_scangle_other 5.424 r_mcangle_it 5.06 r_mcangle_other 5.06 r_scbond_it 3.186 r_scbond_other 3.182 r_mcbond_it 3.057 r_mcbond_other 3.055 r_angle_refined_deg 1.269 r_angle_other_deg 1.179 r_nbd_other 0.311 r_symmetry_nbd_refined 0.243 r_nbd_refined 0.199 r_symmetry_nbd_other 0.187 r_xyhbond_nbd_refined 0.169 r_nbtor_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.13 r_symmetry_nbtor_other 0.093 r_chiral_restr 0.058 r_symmetry_xyhbond_nbd_other 0.007 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2291 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing