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Crystal structure of the oxidized state of Trx1 from Schistosoma japonicum
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% Tassimate (pH 6.5-8.0) and 15-20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.25 45.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.535 α = 90 b = 90.533 β = 90 c = 150.042 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 0.97853 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 2.66 50 95.7 0.97 7.588 3.8 15762
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 2.66 2.71 0.653
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.66 43.375 15107 771 91.425 0.224 0.2211 0.2219 0.2845 0.2847 51.385
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] -0.114 0.467 -0.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.255 r_dihedral_angle_6_deg 15.188 r_dihedral_angle_2_deg 13.667 r_lrange_it 13.017 r_lrange_other 13.017 r_scangle_it 8.411 r_scangle_other 8.41 r_mcangle_it 7.435 r_mcangle_other 7.434 r_dihedral_angle_1_deg 6.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.255 r_dihedral_angle_6_deg 15.188 r_dihedral_angle_2_deg 13.667 r_lrange_it 13.017 r_lrange_other 13.017 r_scangle_it 8.411 r_scangle_other 8.41 r_mcangle_it 7.435 r_mcangle_other 7.434 r_dihedral_angle_1_deg 6.242 r_scbond_it 5.181 r_scbond_other 5.18 r_mcbond_it 4.764 r_mcbond_other 4.746 r_angle_refined_deg 1.539 r_angle_other_deg 0.522 r_xyhbond_nbd_refined 0.316 r_symmetry_xyhbond_nbd_refined 0.238 r_nbd_refined 0.227 r_nbd_other 0.205 r_symmetry_nbd_other 0.204 r_symmetry_nbd_refined 0.184 r_nbtor_refined 0.178 r_ncsr_local_group_3 0.098 r_ncsr_local_group_10 0.096 r_ncsr_local_group_6 0.095 r_ncsr_local_group_8 0.092 r_ncsr_local_group_7 0.086 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_5 0.083 r_ncsr_local_group_9 0.075 r_ncsr_local_group_2 0.074 r_ncsr_local_group_4 0.072 r_ncsr_local_group_1 0.07 r_chiral_restr 0.065 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 4161 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing