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The ligand-free structure of human PPARgamma LBD R288C 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 2.74 59.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.248 α = 90 b = 52.878 β = 90 c = 53.887 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 2017-12-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
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 2.65 50 99.6 0.069 28.03 7.7 11616
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 2.65 2.7 0.759 0.873
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 2.65 49.095 11194 571 97.781 0.241 0.2392 0.2409 0.2753 0.2762 39.247
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] 0.253 0.053 -0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.904 r_dihedral_angle_4_deg 16.518 r_dihedral_angle_3_deg 13.714 r_lrange_it 7.662 r_lrange_other 7.66 r_dihedral_angle_1_deg 6.269 r_scangle_other 5.183 r_scangle_it 5.18 r_mcangle_it 4.473 r_mcangle_other 4.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.904 r_dihedral_angle_4_deg 16.518 r_dihedral_angle_3_deg 13.714 r_lrange_it 7.662 r_lrange_other 7.66 r_dihedral_angle_1_deg 6.269 r_scangle_other 5.183 r_scangle_it 5.18 r_mcangle_it 4.473 r_mcangle_other 4.473 r_scbond_it 3.448 r_scbond_other 3.434 r_mcbond_it 2.627 r_mcbond_other 2.623 r_angle_other_deg 1.447 r_angle_refined_deg 1.244 r_symmetry_xyhbond_nbd_refined 0.313 r_nbd_other 0.308 r_symmetry_nbd_other 0.219 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.169 r_symmetry_nbd_refined 0.111 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_symmetry_xyhbond_nbd_other 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2168 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing