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Crystal structure of thioredoxin gluthathione reductase from Schistosoma japonicum with the U597C mutation in complex with auranofin
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 2.57 52.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.14 α = 90 b = 86.55 β = 90 c = 184.14 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 1.84 50.52 100 0.999 15.7 12.9 117177
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 1.84 1.89 0.645
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 1.84 50.513 117085 5958 99.957 0.192 0.1902 0.2243 38.832
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] -0.818 -0.097 0.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 16.533 r_dihedral_angle_6_deg 15.116 r_dihedral_angle_3_deg 12.88 r_dihedral_angle_2_deg 7.919 r_lrange_other 7.436 r_lrange_it 7.433 r_dihedral_angle_1_deg 6.723 r_scangle_it 6.23 r_scangle_other 6.23 r_scbond_it 4.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 16.533 r_dihedral_angle_6_deg 15.116 r_dihedral_angle_3_deg 12.88 r_dihedral_angle_2_deg 7.919 r_lrange_other 7.436 r_lrange_it 7.433 r_dihedral_angle_1_deg 6.723 r_scangle_it 6.23 r_scangle_other 6.23 r_scbond_it 4.479 r_scbond_other 4.478 r_mcangle_it 4.349 r_mcangle_other 4.349 r_mcbond_it 3.481 r_mcbond_other 3.477 r_angle_refined_deg 1.587 r_angle_other_deg 0.548 r_symmetry_xyhbond_nbd_refined 0.244 r_nbd_refined 0.218 r_symmetry_nbd_other 0.189 r_symmetry_nbd_refined 0.185 r_nbd_other 0.177 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.117 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.081 r_ncsr_local_group_1 0.072 r_dihedral_angle_other_2_deg 0.02 r_bond_refined_d 0.008 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 9050 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing