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Sialidases and Fucosidases of Akkermansia muciniphila are key for rapid growth on colonic mucin and nutrient sharing amongst mucin-associated human gut microbiota
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold alpha fold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.7 293 0.1 M Hepes, 16% PEG10k,
Crystal Properties Matthews coefficient Solvent content 3.16 61.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.19 α = 88.41 b = 76.45 β = 89.08 c = 84.5 γ = 88.23
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 EIGER2 S 16M 2021-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976300 PETRA III, EMBL c/o DESY P14 (MX2)
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 2.7 34.51 90.5 0.08178 0.09486 0.04795 0.998 9.93 3.8 99265 59.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 71 0.745 0.812 0.843 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 alpha fold 2.7 34.51 1.98 47180 2450 90.36 0.2353 0.2331 0.234 0.2754 0.2779 59.87
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 5.7441 f_angle_d 0.8619 f_chiral_restr 0.0508 f_plane_restr 0.0075 f_bond_d 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10602 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction XSCALE data scaling PHASER phasing