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Crystal structure of reduced state of the 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
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 2.68 54.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.44 α = 90 b = 88.16 β = 90 c = 185.516 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 6M 2024-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979460 SSRF BL19U1
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 2.02 50.626 99.9 0.999 14.3 12.9 91695
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 2.03 2.15 0.472
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 2.026 50.626 91689 4585 99.886 0.203 0.2012 0.2459 44.972
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] 0.324 -1.057 0.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.739 r_dihedral_angle_3_deg 13.363 r_lrange_other 8.295 r_lrange_it 8.294 r_dihedral_angle_2_deg 7.469 r_dihedral_angle_1_deg 6.548 r_scangle_it 6.297 r_scangle_other 6.297 r_mcangle_it 4.896 r_mcangle_other 4.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.739 r_dihedral_angle_3_deg 13.363 r_lrange_other 8.295 r_lrange_it 8.294 r_dihedral_angle_2_deg 7.469 r_dihedral_angle_1_deg 6.548 r_scangle_it 6.297 r_scangle_other 6.297 r_mcangle_it 4.896 r_mcangle_other 4.896 r_scbond_it 4.131 r_scbond_other 4.13 r_mcbond_it 3.529 r_mcbond_other 3.529 r_angle_refined_deg 1.555 r_angle_other_deg 0.53 r_symmetry_nbd_refined 0.213 r_nbd_refined 0.208 r_nbd_other 0.206 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.081 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.072 r_ncsr_local_group_1 0.065 r_dihedral_angle_other_2_deg 0.023 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 333 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing