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Crystal structure of Trichuris suis beta-N-acetyl-D-hexosaminidase - HEX-2 in apo form
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 7.5 292 20% PEG 1500
0.15M potasium thiocynate
0.1M Tris pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.17 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.118 α = 90 b = 59.044 β = 114.486 c = 105.977 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M 2022-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97856 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.55 43.74 99.9 0.067 0.08 0.043 0.999 14.1 6.5 17835 59.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.66 99.9 0.782 0.931 0.5 0.843 2.1 6.7
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 2.55 43.74 17268 836 96.734 0.193 0.1894 0.196 0.2594 0.2634 42.658
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] 0.64 -0.307 0.12 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.451 r_dihedral_angle_6_deg 16.771 r_lrange_other 11.454 r_lrange_it 11.452 r_scangle_it 9.331 r_scangle_other 9.329 r_mcangle_it 8.122 r_mcangle_other 8.12 r_dihedral_angle_2_deg 7.398 r_dihedral_angle_1_deg 7.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.451 r_dihedral_angle_6_deg 16.771 r_lrange_other 11.454 r_lrange_it 11.452 r_scangle_it 9.331 r_scangle_other 9.329 r_mcangle_it 8.122 r_mcangle_other 8.12 r_dihedral_angle_2_deg 7.398 r_dihedral_angle_1_deg 7.15 r_scbond_it 6.664 r_scbond_other 6.663 r_mcbond_it 5.855 r_mcbond_other 5.853 r_angle_refined_deg 1.996 r_angle_other_deg 0.64 r_symmetry_xyhbond_nbd_refined 0.322 r_nbd_refined 0.249 r_symmetry_nbd_other 0.238 r_nbtor_refined 0.205 r_nbd_other 0.187 r_xyhbond_nbd_refined 0.159 r_symmetry_nbd_refined 0.126 r_xyhbond_nbd_other 0.093 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3688 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing