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Crystal Structure of Mu class Glutathione-S-Transferase TuGSTm06(Tetur05g05220) in complex with reaction product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8UDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 2.4 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 3.4 63.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.473 α = 90 b = 133.473 β = 90 c = 103.738 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 2022-04-13 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) 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 2.05 40 96.2 0.061 0.398 0.99 20.2 2.3 41596 -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 2.05 2.09 94.7 0.607 0.396 0.733 1.5 2.1
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 2.05 34.603 41594 2003 96.184 0.173 0.1719 0.1804 0.1927 0.2032 42.811
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] -0.952 -0.476 -0.952 3.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.541 r_dihedral_angle_3_deg 13.481 r_dihedral_angle_6_deg 12.404 r_lrange_it 8.601 r_lrange_other 8.578 r_scangle_it 6.451 r_scangle_other 6.45 r_dihedral_angle_1_deg 4.813 r_scbond_other 4.461 r_scbond_it 4.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.541 r_dihedral_angle_3_deg 13.481 r_dihedral_angle_6_deg 12.404 r_lrange_it 8.601 r_lrange_other 8.578 r_scangle_it 6.451 r_scangle_other 6.45 r_dihedral_angle_1_deg 4.813 r_scbond_other 4.461 r_scbond_it 4.458 r_mcangle_other 3.844 r_mcangle_it 3.842 r_mcbond_it 2.719 r_mcbond_other 2.719 r_angle_refined_deg 1.467 r_angle_other_deg 0.756 r_symmetry_nbd_refined 0.298 r_symmetry_xyhbond_nbd_other 0.244 r_nbd_other 0.227 r_symmetry_nbd_other 0.214 r_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.162 r_ncsr_local_group_1 0.105 r_xyhbond_nbd_other 0.095 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3643 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing