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Crystal structure of anthocyanin-related glutathione transferase from poplar in complex with quercetin
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 MICROBATCH 277 Precipitating solution :
- 25 % w/v PEG 4000
- 100 mM MES pH 6.5
- 200 mM MgCl2
Protein solution : 10mg/ml protein in 20 mM Tris pH 8.0
- 5mM DTT
- 10mM L-Cystein
- 2.1mM Quercetin
Crystal Properties Matthews coefficient Solvent content 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.639 α = 90 b = 55.412 β = 119.812 c = 54.894 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 2023-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM07 0.979510 ESRF BM07
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 47.63 95.5 0.027 1 22.6 3.7 43970 13.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 76.5 0.913 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.4 47.629 43948 2267 95.5 0.144 0.1424 0.1424 0.1724 0.1724 22.138
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] -0.035 0.612 -1.193 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.299 r_lrange_it 13.648 r_dihedral_angle_3_deg 12.357 r_scangle_it 11.575 r_mcangle_it 8.605 r_scbond_it 8.426 r_dihedral_angle_2_deg 8.01 r_mcbond_it 6.196 r_dihedral_angle_1_deg 5.661 r_rigid_bond_restr 5.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.299 r_lrange_it 13.648 r_dihedral_angle_3_deg 12.357 r_scangle_it 11.575 r_mcangle_it 8.605 r_scbond_it 8.426 r_dihedral_angle_2_deg 8.01 r_mcbond_it 6.196 r_dihedral_angle_1_deg 5.661 r_rigid_bond_restr 5.485 r_angle_refined_deg 1.978 r_nbtor_refined 0.312 r_nbd_refined 0.215 r_symmetry_nbd_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.133 r_chiral_restr 0.123 r_xyhbond_nbd_refined 0.109 r_gen_planes_refined 0.013 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1718 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing