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Crystal structure of anthocyanin-related glutathione transferase from bilberry
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 277 Precipitating solution :
- 20% v/v Ethylene glycol / 10 % w/v PEG 8000
- 0,1 M Buffer System 1 pH 6,5 (Buffer System 1 : 1.0M, pH6.5 -> Imidazole; MES monohydrate (acid))
- 0,1 M Amino acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine)
Protein solution : 14.9 mg/mL protein in 20 mM Tris-HCl pH 8.0 ; 200 mM NaCl ; 1mM EDTA
Crystal Properties Matthews coefficient Solvent content 2.76 55.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.294 α = 90 b = 159.117 β = 95.601 c = 90.374 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 4M 2022-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967697 ESRF MASSIF-3
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 2.34 89.94 98.8 0.105 0.992 4.8 3.5 65742
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 2.34 2.4 99 0.637 0.612 1.1 3.7
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 2.34 89.94 65706 3282 98.72 0.212 0.2103 0.2103 0.2426 0.2427 48.692
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] -0.767 -1.228 0.502 0.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.848 r_dihedral_angle_6_deg 14.788 r_lrange_it 12.873 r_scangle_it 10.57 r_mcangle_it 8.816 r_scbond_it 7.076 r_dihedral_angle_1_deg 6.339 r_dihedral_angle_2_deg 6.193 r_mcbond_it 5.76 r_angle_refined_deg 1.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.848 r_dihedral_angle_6_deg 14.788 r_lrange_it 12.873 r_scangle_it 10.57 r_mcangle_it 8.816 r_scbond_it 7.076 r_dihedral_angle_1_deg 6.339 r_dihedral_angle_2_deg 6.193 r_mcbond_it 5.76 r_angle_refined_deg 1.854 r_nbtor_refined 0.305 r_symmetry_nbd_refined 0.259 r_nbd_refined 0.22 r_symmetry_xyhbond_nbd_refined 0.184 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.136 r_ncsr_local_group_7 0.08 r_ncsr_local_group_4 0.079 r_ncsr_local_group_5 0.079 r_ncsr_local_group_1 0.076 r_ncsr_local_group_2 0.076 r_ncsr_local_group_3 0.076 r_ncsr_local_group_6 0.076 r_ncsr_local_group_13 0.075 r_ncsr_local_group_9 0.074 r_ncsr_local_group_11 0.074 r_ncsr_local_group_15 0.073 r_ncsr_local_group_14 0.07 r_ncsr_local_group_8 0.069 r_ncsr_local_group_10 0.067 r_ncsr_local_group_12 0.066 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10259 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing