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Crystal Structure of Mu class GST from 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 293 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.36 47.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.464 α = 90 b = 60.464 β = 90 c = 234.998 γ = 120
Symmetry Space Group P 31 2 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 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 2.75 40 99.7 0.143 0.046 0.989 18 9.5 13765 -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 2.75 2.8 100 0.782 0.273 0.73 2.5 7.8
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 2.75 39.197 13676 714 99.687 0.217 0.2149 0.22 0.2613 0.266 35.729
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] -1.514 -0.757 -1.514 4.911
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.852 r_dihedral_angle_6_deg 12.524 r_dihedral_angle_2_deg 11.103 r_dihedral_angle_1_deg 5.331 r_lrange_other 5.22 r_lrange_it 5.219 r_scangle_it 2.085 r_scangle_other 2.084 r_mcangle_it 1.673 r_mcangle_other 1.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.852 r_dihedral_angle_6_deg 12.524 r_dihedral_angle_2_deg 11.103 r_dihedral_angle_1_deg 5.331 r_lrange_other 5.22 r_lrange_it 5.219 r_scangle_it 2.085 r_scangle_other 2.084 r_mcangle_it 1.673 r_mcangle_other 1.673 r_scbond_it 1.429 r_scbond_other 1.396 r_angle_refined_deg 1.236 r_mcbond_it 0.945 r_mcbond_other 0.945 r_angle_other_deg 0.659 r_nbd_other 0.281 r_symmetry_nbd_other 0.212 r_nbd_refined 0.207 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.158 r_ncsr_local_group_1 0.124 r_symmetry_nbd_refined 0.115 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_refined 0.075 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3600 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing