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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, HANGING DROP 291.15 0.02M DL-Arginine hydrochloride, 0.02M DL-Threonine, 0.02M DL-Histidine monohydrochloride monohydrate, 0.02M DL-5-Hydroxylysine hydrochloride, 0.02M trans-4-hydroxy-L-proline, 0.1 M MOPSO, 0.1 M Bis-Tris pH 6.5, 15% w/v PEG 3000, 20% v/v 1, 2, 4-Butanetriol and 2% w/v NDSB 256.
Crystal Properties Matthews coefficient Solvent content 2.96 58.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.79 α = 90 b = 67.91 β = 132.15 c = 140.82 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 2024-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.07 71.46 99.5 0.175 0.994 8.6 3.2 25445
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.07 3.15 0.992 0.744 1.8
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 3.07 71.46 1.35 25404 1239 99.32 0.2326 0.2287 0.2486 0.3105 0.3062
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 7.49 f_angle_d 1.155 f_chiral_restr 0.058 f_plane_restr 0.014 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7245 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 91
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction MOLREP phasing