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The ligand-free structure of human PPARgamma ligand-binding domain R288A 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 6JQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 296 2.2 M sodium malonate (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.72 54.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.47 α = 90 b = 52.696 β = 90 c = 53.669 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 2015-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 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 2.7 50 99.6 0.079 41.1 9.5 10775
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 2.7 2.75 100 0.704
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 6JQ7 2.7 30.002 10735 551 99.49 0.219 0.2166 0.2223 0.2575 0.2639 72.077
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] -4.565 1.978 2.587
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.336 r_dihedral_angle_4_deg 24.745 r_dihedral_angle_3_deg 16.014 r_lrange_other 12.44 r_lrange_it 12.439 r_scangle_it 8.726 r_scangle_other 8.72 r_mcangle_it 7.148 r_mcangle_other 7.145 r_scbond_it 5.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.336 r_dihedral_angle_4_deg 24.745 r_dihedral_angle_3_deg 16.014 r_lrange_other 12.44 r_lrange_it 12.439 r_scangle_it 8.726 r_scangle_other 8.72 r_mcangle_it 7.148 r_mcangle_other 7.145 r_scbond_it 5.415 r_scbond_other 5.409 r_dihedral_angle_1_deg 4.66 r_mcbond_it 4.602 r_mcbond_other 4.598 r_angle_refined_deg 1.314 r_angle_other_deg 1.213 r_nbd_other 0.38 r_symmetry_nbd_refined 0.335 r_symmetry_xyhbond_nbd_refined 0.254 r_nbd_refined 0.211 r_symmetry_nbd_other 0.199 r_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.16 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.057 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2174 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing