☰ Navigation Tabs
Crystal structure of thioredoxin gluthathione reductase from Schistosoma japonicum with the U597C mutation SjTGR-U597C
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 2.59 52.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.38 α = 90 b = 86.83 β = 90 c = 184.47 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 2.16 50.65 100 0.999 14.5 12.9 73462
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 2.16 2.22 0.649
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 2.16 50.647 73369 3626 99.916 0.193 0.1912 0.2294 48.233
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] -1.093 -0.201 1.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.117 r_dihedral_angle_3_deg 13.487 r_dihedral_angle_2_deg 7.866 r_lrange_other 7.855 r_lrange_it 7.854 r_dihedral_angle_1_deg 7.039 r_scangle_it 6.662 r_scangle_other 6.661 r_mcangle_it 4.833 r_mcangle_other 4.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.117 r_dihedral_angle_3_deg 13.487 r_dihedral_angle_2_deg 7.866 r_lrange_other 7.855 r_lrange_it 7.854 r_dihedral_angle_1_deg 7.039 r_scangle_it 6.662 r_scangle_other 6.661 r_mcangle_it 4.833 r_mcangle_other 4.832 r_scbond_it 4.576 r_scbond_other 4.576 r_mcbond_it 3.676 r_mcbond_other 3.675 r_angle_refined_deg 1.542 r_angle_other_deg 0.523 r_symmetry_xyhbond_nbd_refined 0.266 r_nbd_other 0.218 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.208 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_other 0.119 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.072 r_ncsr_local_group_1 0.072 r_dihedral_angle_other_2_deg 0.053 r_bond_refined_d 0.006 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 9044 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing