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Crystal structure of anthocyanin-related GSTF8 from Populus trichocarpa in complex with (-)-catechin and glutathione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 277 1 part protein solution (30mM Tris pH 8, 200mM NaCl, 1mM EDTA)
1 part buffer (100mM MES pH 6.4, 200mM MgCl2, 17.9% PEG200)
Crystal Properties Matthews coefficient Solvent content 2.56 51.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.948 α = 90 b = 55.447 β = 113.55 c = 54.787 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 2M 2020-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999995 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.093 38.496 99.2 0.051 0.055 0.999 15.7 6.4 101092
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.093 1.11 0.608 0.667 0.817 2.3
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 5F07 1.093 38.496 100738 4917 98.833 0.133 0.1324 0.133 0.1488 0.1492 14.844
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] 0.062 0.703 -0.702 0.02
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 24.941 r_dihedral_angle_6_deg 17.525 r_dihedral_angle_3_deg 12.937 r_scbond_it 11.445 r_scbond_other 11.44 r_dihedral_angle_2_deg 8.589 r_scangle_it 7.808 r_scangle_other 7.805 r_lrange_it 6.943 r_lrange_other 6.731
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 24.941 r_dihedral_angle_6_deg 17.525 r_dihedral_angle_3_deg 12.937 r_scbond_it 11.445 r_scbond_other 11.44 r_dihedral_angle_2_deg 8.589 r_scangle_it 7.808 r_scangle_other 7.805 r_lrange_it 6.943 r_lrange_other 6.731 r_dihedral_angle_1_deg 5.997 r_mcangle_it 3.533 r_mcangle_other 3.532 r_mcbond_it 2.808 r_mcbond_other 2.807 r_angle_refined_deg 1.727 r_angle_other_deg 0.626 r_symmetry_nbd_refined 0.377 r_symmetry_xyhbond_nbd_refined 0.331 r_nbd_refined 0.242 r_nbd_other 0.232 r_xyhbond_nbd_refined 0.22 r_nbtor_refined 0.192 r_symmetry_nbd_other 0.189 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1718 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing