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Crystal structure of the reduced 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 5mM DTT, 4% Tassimate (pH 6.5-8.0) and 15-20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.916 α = 90 b = 90.859 β = 90 c = 151.372 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 0.979183 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 1.89 50 96.7 0.999 11.91 9.6 43078
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 2.01 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.898 45.43 43078 2154 96.731 0.223 0.2211 0.2285 0.2538 0.2583 46.849
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] 0.855 0.426 -1.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.621 r_dihedral_angle_6_deg 13.957 r_lrange_it 10.221 r_lrange_other 10.216 r_dihedral_angle_2_deg 8.657 r_scangle_it 7.967 r_scangle_other 7.966 r_mcangle_it 6.025 r_mcangle_other 6.024 r_dihedral_angle_1_deg 5.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.621 r_dihedral_angle_6_deg 13.957 r_lrange_it 10.221 r_lrange_other 10.216 r_dihedral_angle_2_deg 8.657 r_scangle_it 7.967 r_scangle_other 7.966 r_mcangle_it 6.025 r_mcangle_other 6.024 r_dihedral_angle_1_deg 5.795 r_scbond_it 5.051 r_scbond_other 5.05 r_mcbond_it 4.017 r_mcbond_other 4.017 r_angle_refined_deg 1.568 r_angle_other_deg 0.516 r_nbd_refined 0.224 r_nbd_other 0.217 r_xyhbond_nbd_refined 0.196 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.132 r_ncsr_local_group_3 0.098 r_ncsr_local_group_6 0.095 r_ncsr_local_group_10 0.094 r_ncsr_local_group_8 0.09 r_ncsr_local_group_5 0.089 r_ncsr_local_group_7 0.089 r_ncsr_local_group_2 0.088 r_ncsr_local_group_4 0.083 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_9 0.076 r_ncsr_local_group_1 0.073 r_chiral_restr 0.07 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 4169 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing