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Crystal Structure of Mu class Glutathione-S-Transferase, TuGSTm06(Tetur05g05220) 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 8 293 2 M ammonium sulfate, 0.1 M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 3.25 62.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.802 α = 90 b = 135.802 β = 90 c = 191.998 γ = 120
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 2021-12-13 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) 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 2.25 40 99.5 0.094 0.04 23.9 5.3 62541 -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 2.25 2.29 0.586 0.251 0.773 2.4
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 2.25 39.233 62374 3135 99.523 0.199 0.1967 0.2037 0.2357 0.2416 63.802
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] 0.372 0.186 0.372 -1.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.033 r_dihedral_angle_3_deg 13.919 r_dihedral_angle_2_deg 11.714 r_lrange_other 9.775 r_lrange_it 9.761 r_scangle_it 9.134 r_scangle_other 8.742 r_scbond_it 6.785 r_scbond_other 6.485 r_mcangle_other 6.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.033 r_dihedral_angle_3_deg 13.919 r_dihedral_angle_2_deg 11.714 r_lrange_other 9.775 r_lrange_it 9.761 r_scangle_it 9.134 r_scangle_other 8.742 r_scbond_it 6.785 r_scbond_other 6.485 r_mcangle_other 6.054 r_mcangle_it 6.053 r_dihedral_angle_1_deg 6.019 r_mcbond_it 4.841 r_mcbond_other 4.838 r_angle_refined_deg 1.389 r_angle_other_deg 0.745 r_symmetry_nbd_refined 0.258 r_nbd_other 0.235 r_nbd_refined 0.215 r_symmetry_nbd_other 0.211 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.167 r_ncsr_local_group_3 0.089 r_ncsr_local_group_2 0.086 r_ncsr_local_group_5 0.082 r_ncsr_local_group_4 0.08 r_symmetry_nbtor_other 0.075 r_ncsr_local_group_1 0.074 r_symmetry_xyhbond_nbd_other 0.072 r_chiral_restr 0.067 r_ncsr_local_group_6 0.063 r_gen_planes_other 0.011 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7267 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing