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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 experimental model PDB 8UDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M magnesium chloride hexahydrate, 0.1M Tris pH 8.5, and 25% w/v polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.34 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.492 α = 90 b = 69.918 β = 90 c = 118.05 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 EIGER X 16M 2021-08-03 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 2.65 40 98.8 0.061 0.023 0.998 29 6.9 14919 -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 2.65 2.71 86.1 0.667 0.297 0.829 1.5 4.2
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 2.65 35.967 14739 706 98.933 0.215 0.2124 0.2134 0.2617 0.2627 82.664
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] -0.536 -1.105 1.641
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.456 r_dihedral_angle_3_deg 14.225 r_dihedral_angle_6_deg 11.448 r_lrange_other 10.203 r_lrange_it 10.201 r_scangle_it 6.784 r_scangle_other 6.783 r_mcangle_it 6.259 r_mcangle_other 6.258 r_dihedral_angle_1_deg 5.468
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.456 r_dihedral_angle_3_deg 14.225 r_dihedral_angle_6_deg 11.448 r_lrange_other 10.203 r_lrange_it 10.201 r_scangle_it 6.784 r_scangle_other 6.783 r_mcangle_it 6.259 r_mcangle_other 6.258 r_dihedral_angle_1_deg 5.468 r_scbond_it 4.582 r_scbond_other 4.578 r_mcbond_it 4.06 r_mcbond_other 4.056 r_angle_refined_deg 1.319 r_angle_other_deg 0.683 r_nbd_refined 0.232 r_nbd_other 0.218 r_symmetry_nbd_other 0.216 r_symmetry_xyhbond_nbd_refined 0.203 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.139 r_ncsr_local_group_1 0.129 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3424 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing