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The ligand-free structure of human PPARgamma LBD Q286E 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 2.8 56.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.442 α = 90 b = 52.126 β = 90 c = 54.417 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 2018-07-23 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) 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 2.25 50 100 0.98 19.28 7.9 18418
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 2.25 2.29 100 0.87 2.81 8.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5GTP 2.3 48.399 17003 1718 99.806 0.217 0.212 0.257 0.249 34.35
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] 0.042 0.126 -0.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.648 r_dihedral_angle_4_deg 19.814 r_dihedral_angle_3_deg 15.102 r_dihedral_angle_1_deg 6.005 r_lrange_other 5.879 r_lrange_it 5.878 r_scangle_it 3.497 r_scangle_other 3.496 r_mcangle_it 3.307 r_mcangle_other 3.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.648 r_dihedral_angle_4_deg 19.814 r_dihedral_angle_3_deg 15.102 r_dihedral_angle_1_deg 6.005 r_lrange_other 5.879 r_lrange_it 5.878 r_scangle_it 3.497 r_scangle_other 3.496 r_mcangle_it 3.307 r_mcangle_other 3.305 r_scbond_it 2.004 r_scbond_other 1.992 r_mcbond_it 1.952 r_mcbond_other 1.952 r_angle_refined_deg 1.261 r_angle_other_deg 1.219 r_nbd_other 0.272 r_nbd_refined 0.193 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.167 r_nbtor_refined 0.154 r_symmetry_nbd_refined 0.129 r_symmetry_xyhbond_nbd_refined 0.094 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.061 r_symmetry_xyhbond_nbd_other 0.006 r_bond_refined_d 0.004 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 2301 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing