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Crystal structure of thioredoxin gluthathione reductase from Schistosoma japonicum with the U597C mutation in complex with NADPH
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 2.56 52.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.22 α = 90 b = 86.36 β = 90 c = 183.59 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 2023-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97923 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 1.9 61.2 100 0.999 16.6 12.8 106193
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 1.9 1.95 0.727
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 1.9 60.368 106103 5351 99.978 0.192 0.1898 0.2273 32.766
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] -0.729 -1.15 1.879
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.86 r_dihedral_angle_other_2_deg 12.574 r_dihedral_angle_3_deg 12.386 r_dihedral_angle_2_deg 8.232 r_dihedral_angle_1_deg 6.789 r_lrange_other 6.714 r_lrange_it 6.71 r_scangle_it 5.518 r_scangle_other 5.518 r_scbond_it 3.738
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.86 r_dihedral_angle_other_2_deg 12.574 r_dihedral_angle_3_deg 12.386 r_dihedral_angle_2_deg 8.232 r_dihedral_angle_1_deg 6.789 r_lrange_other 6.714 r_lrange_it 6.71 r_scangle_it 5.518 r_scangle_other 5.518 r_scbond_it 3.738 r_scbond_other 3.737 r_mcangle_it 3.606 r_mcangle_other 3.605 r_mcbond_it 2.739 r_mcbond_other 2.739 r_angle_refined_deg 1.532 r_angle_other_deg 0.535 r_symmetry_nbd_refined 0.247 r_nbd_other 0.246 r_nbd_refined 0.217 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.17 r_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.077 r_ncsr_local_group_1 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_symmetry_xyhbond_nbd_other 0.003 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 539 Heterogen Atoms 182
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing