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Crystal structure of thioredoxin gluthathione reductase from Schistosoma japonicum SjTGR-WT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A4Z2CZE1-F1 TGR
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 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.615 α = 90 b = 86.266 β = 90 c = 182.093 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 EIGER2 S 9M 2024-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.919082 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 2.557 91.05 99.9 0.988 6.6 8.3 43384
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 2.557 2.69 0.366
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 2.557 91.047 43204 2157 99.537 0.21 0.2069 0.2599 50.865
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] -0.508 1.351 -0.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.58 r_dihedral_angle_6_deg 14.379 r_dihedral_angle_2_deg 10.662 r_lrange_it 9.433 r_lrange_other 9.433 r_scangle_it 7.315 r_scangle_other 7.315 r_dihedral_angle_1_deg 7.174 r_mcangle_it 6.645 r_mcangle_other 6.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.58 r_dihedral_angle_6_deg 14.379 r_dihedral_angle_2_deg 10.662 r_lrange_it 9.433 r_lrange_other 9.433 r_scangle_it 7.315 r_scangle_other 7.315 r_dihedral_angle_1_deg 7.174 r_mcangle_it 6.645 r_mcangle_other 6.644 r_scbond_it 4.899 r_scbond_other 4.899 r_mcbond_it 4.524 r_mcbond_other 4.523 r_angle_refined_deg 1.656 r_angle_other_deg 0.557 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.22 r_nbd_other 0.208 r_symmetry_nbd_other 0.19 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.168 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_1 0.077 r_chiral_restr 0.074 r_dihedral_angle_other_2_deg 0.024 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9056 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing