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Crystal structure of thioredoxin gluthathione reductase from Schistosoma japonicum with the U597C mutation in complex with GSH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295.15 4% Tacsimate (pH 6.5-8.0) and 15-20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.64 53.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.56 α = 90 b = 87.58 β = 90 c = 185.6 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 PILATUS 2M 2023-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979183 SSRF BL10U2
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 2.12 50.928 100 0.998 14.5 12.8 78985
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 2.12 2.18 0.608
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 FREE R-VALUE 2.12 50.928 78905 3952 99.961 0.211 0.2089 0.2479 55.449
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] -1.388 0.251 1.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.443 r_dihedral_angle_3_deg 14.308 r_lrange_other 9.788 r_lrange_it 9.785 r_dihedral_angle_2_deg 9.72 r_scangle_it 8.616 r_scangle_other 8.615 r_mcangle_it 7.572 r_mcangle_other 7.571 r_dihedral_angle_1_deg 7.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.443 r_dihedral_angle_3_deg 14.308 r_lrange_other 9.788 r_lrange_it 9.785 r_dihedral_angle_2_deg 9.72 r_scangle_it 8.616 r_scangle_other 8.615 r_mcangle_it 7.572 r_mcangle_other 7.571 r_dihedral_angle_1_deg 7.266 r_scbond_it 6.189 r_scbond_other 6.188 r_mcbond_it 5.8 r_mcbond_other 5.8 r_dihedral_angle_other_2_deg 5.242 r_angle_refined_deg 1.784 r_angle_other_deg 0.606 r_nbd_refined 0.22 r_nbd_other 0.216 r_symmetry_xyhbond_nbd_refined 0.206 r_symmetry_nbd_refined 0.199 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.178 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_1 0.079 r_symmetry_xyhbond_nbd_other 0.027 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9044 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing