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Crystal structure of the oxidized state of thioredoxin gluthathione reductase from Schistosoma japonicum with the U597C mutation SjTGR-U597C-oxidized
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A4Z2CZE1-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295.15 4% Tassimate (pH 6.5-8.0) and 15-20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.81 α = 90 b = 86.616 β = 90 c = 182.579 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 295.15 PIXEL DECTRIS EIGER2 S 9M 2024-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979183 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.07 91.29 100 0.998 11.4 11.7 81335
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.19 0.454
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-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 2.074 91.29 81189 3903 99.913 0.195 0.1928 0.2389 43.208
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] -0.336 -0.237 0.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.535 r_dihedral_angle_3_deg 13.719 r_dihedral_angle_2_deg 8.226 r_lrange_other 8.132 r_lrange_it 8.131 r_dihedral_angle_1_deg 7.302 r_scangle_it 6.568 r_scangle_other 6.568 r_mcangle_it 5.129 r_mcangle_other 5.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.535 r_dihedral_angle_3_deg 13.719 r_dihedral_angle_2_deg 8.226 r_lrange_other 8.132 r_lrange_it 8.131 r_dihedral_angle_1_deg 7.302 r_scangle_it 6.568 r_scangle_other 6.568 r_mcangle_it 5.129 r_mcangle_other 5.128 r_scbond_it 4.526 r_scbond_other 4.526 r_mcbond_it 3.805 r_mcbond_other 3.803 r_angle_refined_deg 1.698 r_angle_other_deg 0.568 r_nbd_other 0.244 r_symmetry_xyhbond_nbd_other 0.239 r_symmetry_nbd_refined 0.231 r_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.211 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.166 r_dihedral_angle_other_2_deg 0.114 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.077 r_metal_ion_refined 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9048 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing