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A novel allosteric covalent inhibitory site of fucosyltransferase 8 revealed by crystal structures
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X5S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.001M Rubidium chloride, 0.001M Strontium acetate, 0.001M Cesium acetate, 0.001M Barium acetate, 0.1 M MOPSO, 0.1 M Bis-Tris pH 6.5, 12.5% w/v PEG 4000 and 20% w/v 1,2,6-Hexanetriol.
Crystal Properties Matthews coefficient Solvent content 2.78 55.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.514 α = 90 b = 70.242 β = 118.61 c = 105.606 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 STFC Large Pixel Detector 2023-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 2.49 86.26 98.7 0.109 0.124 0.058 0.982 10.5 4.3 43902
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 2.49 2.63 99.5 0.56 0.661 0.344 0.778 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.49 51.95 1.35 43879 2180 98.62 0.1869 0.1844 0.1877 0.2347 0.2348
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.815 f_angle_d 0.951 f_chiral_restr 0.05 f_plane_restr 0.009 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7189 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement Aimless data scaling autoPROC data reduction MOLREP phasing