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Crystal Structure of Mu class Glutathione-S-Transferase, TuGSTm12(Tetur05g05300) from Tetranychus urticae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.1 M sodium malonate pH 6.0 and 12% w/v polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.34 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.086 α = 90 b = 60.086 β = 90 c = 472.821 γ = 120
Symmetry Space Group P 61 2 2
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 EIGER2 X 16M 2022-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 40 93.8 0.117 0.037 0.997 31.2 10.8 13059 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 100 1.012 0.256 0.753 2 15.2
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 2.8 39.056 12870 664 93.928 0.214 0.2111 0.2158 0.2709 0.2819 107.875
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] 0.314 0.157 0.314 -1.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.87 r_lrange_it 15.857 r_dihedral_angle_3_deg 13.559 r_dihedral_angle_6_deg 11.009 r_scangle_it 10.322 r_mcangle_it 8.362 r_scbond_it 7.272 r_mcbond_it 5.834 r_dihedral_angle_1_deg 5.536 r_angle_refined_deg 1.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.87 r_lrange_it 15.857 r_dihedral_angle_3_deg 13.559 r_dihedral_angle_6_deg 11.009 r_scangle_it 10.322 r_mcangle_it 8.362 r_scbond_it 7.272 r_mcbond_it 5.834 r_dihedral_angle_1_deg 5.536 r_angle_refined_deg 1.283 r_nbtor_refined 0.319 r_nbd_refined 0.224 r_symmetry_nbd_refined 0.198 r_symmetry_xyhbond_nbd_refined 0.134 r_xyhbond_nbd_refined 0.131 r_ncsr_local_group_1 0.12 r_chiral_restr 0.084 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3528 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing