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The agonist-free structure of human PPARgamma ligand binding domain in the presence of the SRC-1 coactivator peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VN2
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 2.73 54.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.31 α = 90 b = 53.062 β = 90 c = 53.552 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 2014-05-21 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) 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 99.4 36.2 5.8 16193
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 2.35 2.39 100 0.603 4 6.1
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3VN2 2.35 30 15328 817 99.43 0.21292 0.21066 0.25809 0.2638 RANDOM 67.958
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] -2.54 0.82 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.648 r_dihedral_angle_4_deg 22.439 r_dihedral_angle_3_deg 14.4 r_long_range_B_refined 11.45 r_long_range_B_other 11.449 r_scangle_other 8.449 r_mcangle_it 7.147 r_mcangle_other 7.145 r_dihedral_angle_1_deg 5.614 r_scbond_it 5.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.648 r_dihedral_angle_4_deg 22.439 r_dihedral_angle_3_deg 14.4 r_long_range_B_refined 11.45 r_long_range_B_other 11.449 r_scangle_other 8.449 r_mcangle_it 7.147 r_mcangle_other 7.145 r_dihedral_angle_1_deg 5.614 r_scbond_it 5.282 r_scbond_other 5.281 r_mcbond_it 4.82 r_mcbond_other 4.817 r_angle_refined_deg 1.496 r_angle_other_deg 1.181 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2196 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing