☰ Navigation Tabs
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 alphafold model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 293 18% PEG 3350,0.1 M BIS TRIS, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.48 50.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.07 α = 90 b = 51.78 β = 93.07 c = 118.44 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 S 16M 2022-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976254 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 1.3 59.135 99.7 0.066 0.069 0.999 12.14 5.5 308465 16.71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.33 97.1 1.7 1 0.44 0.8 4
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 alphafold model 1.3 50.25 1.33 296679 14930 97.67 0.1672 0.1661 0.1733 0.1876 0.1944 23.41
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 8.1742 f_angle_d 1.2238 f_chiral_restr 0.0956 f_plane_restr 0.0144 f_bond_d 0.0116
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8999 Nucleic Acid Atoms Solvent Atoms 1416 Heterogen Atoms 130
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction XSCALE data scaling PHASER phasing