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Crystal structure of anthocyanin-related glutathione transferase from bilberry in complex with glutathione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5707
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 Precipitating solution :
- 25% PEG 4000
- 10% MPD 10%
- 100 mM MES pH 6.5
Protein solution :
- 10 mg/mL protein in Tris-HCl 30 mM pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.16 43.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.881 α = 90 b = 82.904 β = 90 c = 91.675 γ = 90
Symmetry Space Group P 21 21 21
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 2025-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM07 0.979506 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 1.8 47.72 99.2 0.077 1 8.9 4.1 39704
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 98.7 0.567 0.63 1.7
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 1.802 47.715 39659 1960 98.888 0.173 0.1709 0.1709 0.2145 0.2146 21.832
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] -0.521 -1.528 2.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.862 r_dihedral_angle_3_deg 14.8 r_dihedral_angle_2_deg 10.535 r_lrange_it 7.739 r_lrange_other 7.719 r_dihedral_angle_1_deg 6.38 r_scangle_it 6.312 r_scangle_other 6.311 r_scbond_it 4.316 r_scbond_other 4.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.862 r_dihedral_angle_3_deg 14.8 r_dihedral_angle_2_deg 10.535 r_lrange_it 7.739 r_lrange_other 7.719 r_dihedral_angle_1_deg 6.38 r_scangle_it 6.312 r_scangle_other 6.311 r_scbond_it 4.316 r_scbond_other 4.315 r_mcangle_it 3.35 r_mcangle_other 3.349 r_mcbond_it 2.613 r_mcbond_other 2.608 r_angle_refined_deg 1.964 r_angle_other_deg 0.66 r_nbd_other 0.235 r_symmetry_nbd_refined 0.232 r_nbd_refined 0.227 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.151 r_symmetry_xyhbond_nbd_refined 0.149 r_ncsr_local_group_1 0.111 r_chiral_restr 0.108 r_metal_ion_refined 0.09 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3417 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing