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Crystal structure of the oxidized state of TRP14 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 289.15 0.2 M lithium sulfate monohydrate, 0.1 M HEPES (pH 5.5), and 25% polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 1.95 36.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.631 α = 90 b = 54.833 β = 90 c = 37.751 γ = 90
Symmetry Space Group P 21 21 2
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 1.69 37.97 100 0.999 15.3 11.5 12749
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 1.69 1.73 0.484
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 1.692 37.97 12719 589 99.953 0.203 0.2017 0.207 0.2423 0.2482 28.948
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] 0.996 -0.112 -0.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.921 r_dihedral_angle_6_deg 12.827 r_dihedral_angle_2_deg 7.837 r_dihedral_angle_1_deg 6.37 r_lrange_it 6.265 r_lrange_other 6.264 r_scangle_it 5.559 r_scangle_other 5.555 r_scbond_it 3.791 r_scbond_other 3.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.921 r_dihedral_angle_6_deg 12.827 r_dihedral_angle_2_deg 7.837 r_dihedral_angle_1_deg 6.37 r_lrange_it 6.265 r_lrange_other 6.264 r_scangle_it 5.559 r_scangle_other 5.555 r_scbond_it 3.791 r_scbond_other 3.77 r_mcangle_other 3.754 r_mcangle_it 3.75 r_mcbond_it 2.651 r_mcbond_other 2.65 r_angle_refined_deg 1.729 r_angle_other_deg 0.587 r_symmetry_xyhbond_nbd_refined 0.286 r_nbd_refined 0.235 r_nbd_other 0.216 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.185 r_symmetry_nbd_refined 0.128 r_symmetry_nbtor_other 0.093 r_chiral_restr 0.081 r_xyhbond_nbd_other 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 974 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing