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The ligand-free structure of human PPARgamma LBD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VSO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 1.2 M Sodium citrate tribasic dihydrate, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.62 53.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.15 α = 90 b = 62.256 β = 102.508 c = 119.504 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2019-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.97941 PAL/PLS 11C
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 2.1 30 98 0.101 12.625 4.6 38322
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 2.1 2.14 0.583
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 3VSO 2.102 29.345 35593 1769 90.889 0.221 0.2181 0.2232 0.2675 0.2712 29.241
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] 0.357 -0.048 0.133 -0.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.651 r_dihedral_angle_4_deg 17.137 r_dihedral_angle_3_deg 13.383 r_dihedral_angle_1_deg 5.288 r_lrange_it 4.953 r_lrange_other 4.945 r_scangle_it 2.445 r_scangle_other 2.444 r_mcangle_it 2.339 r_mcangle_other 2.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.651 r_dihedral_angle_4_deg 17.137 r_dihedral_angle_3_deg 13.383 r_dihedral_angle_1_deg 5.288 r_lrange_it 4.953 r_lrange_other 4.945 r_scangle_it 2.445 r_scangle_other 2.444 r_mcangle_it 2.339 r_mcangle_other 2.338 r_angle_other_deg 2.221 r_scbond_it 1.443 r_scbond_other 1.443 r_mcbond_it 1.352 r_mcbond_other 1.352 r_angle_refined_deg 1.198 r_nbd_other 0.26 r_symmetry_nbd_refined 0.22 r_symmetry_nbd_other 0.205 r_symmetry_xyhbond_nbd_refined 0.203 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.15 r_symmetry_xyhbond_nbd_other 0.058 r_symmetry_nbtor_other 0.056 r_chiral_restr 0.05 r_bond_other_d 0.034 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4208 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing