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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 0.01M Spermine tetrahydrochloride, 0.01M Spermidine trihydrochloride, 0.01M 1,4-Diaminobutane dihydrochloride, 0.01M DL-Ornithine monohydrochloride, 0.01 M MOPSO, 0.1 M Bis-Tris pH 6.5, 10% w/v PEG 8000 and 20% v/v 1,5-Pentanediol.
Crystal Properties Matthews coefficient Solvent content 3.05 59.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.43 α = 90 b = 69.74 β = 132.62 c = 141.69 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 291.15 PIXEL STFC Large Pixel Detector 2023-10-23 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 2.66 32.24 99.6 0.07 0.994 10.4 3.6 40090
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 2.66 2.73 0.943 0.56 3.8
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 2.66 30.86 1.34 40020 2074 99.42 0.2186 0.2157 0.2184 0.2712 0.2709
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 7.153 f_angle_d 1.04 f_chiral_restr 0.055 f_plane_restr 0.011 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7201 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data scaling xia2 data reduction MOLREP phasing