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Crystal structure of hPPARgamma ligand binding domain complexed with rosiglitazone-based fluorescence probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VV3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 One microliter of PPARgamma-LBD solution (6 mg/mL, in 20 mM Tris-HCl pH 8.0, 1 mM TCEP, 0.5 mM EDTA) with 0.5 equiv. ligand with 1 microliter of reservoir solution (0.8 M sodium citrate and 0.1 M Tris-HCl pH 7.3). Drops were equilibrated against 300 microliter of reservoir solution at 293K.
Crystal Properties Matthews coefficient Solvent content 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.33 α = 90 b = 61.9 β = 102.29 c = 119.37 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 PILATUS3 S 2M 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 26.75 99.1 0.043 0.06 0.042 0.998 14.1 3 29512
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 0.348 0.481 0.331 0.858 2.9
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 2vv3 2.3 26.75 29502 1515 98.904 0.226 0.2243 0.2644 0.2833 49.828
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] -0.595 0.453 0.218 0.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.232 r_dihedral_angle_4_deg 20.541 r_dihedral_angle_3_deg 19.355 r_dihedral_angle_1_deg 6.761 r_lrange_it 4.794 r_lrange_other 4.792 r_scangle_it 3.427 r_scangle_other 3.427 r_mcangle_other 2.658 r_mcangle_it 2.657
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.232 r_dihedral_angle_4_deg 20.541 r_dihedral_angle_3_deg 19.355 r_dihedral_angle_1_deg 6.761 r_lrange_it 4.794 r_lrange_other 4.792 r_scangle_it 3.427 r_scangle_other 3.427 r_mcangle_other 2.658 r_mcangle_it 2.657 r_scbond_it 2.211 r_scbond_other 2.21 r_angle_refined_deg 1.886 r_mcbond_it 1.774 r_mcbond_other 1.748 r_angle_other_deg 1.378 r_nbd_refined 0.235 r_symmetry_nbd_refined 0.229 r_nbd_other 0.223 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.122 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4058 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement Aimless data scaling pointless data reduction PHASER phasing Coot model building