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Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ILN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 200 mM sodium malonate pH 7.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.22 61.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.646 α = 90 b = 82.646 β = 90 c = 121.489 γ = 90
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 PILATUS 6M 2018-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.05 82.65 100 0.986 6.3 7.4 51105
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.16 0.958 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3ILN 2.05 82.646 51036 2613 99.941 0.202 0.1994 0.2064 0.2402 0.2445 41.008
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] -0.382 -0.382 0.765
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.37 r_dihedral_angle_4_deg 16.039 r_dihedral_angle_3_deg 15.177 r_dihedral_angle_1_deg 8.58 r_lrange_it 4.191 r_lrange_other 4.175 r_scangle_it 2.454 r_scangle_other 2.454 r_mcangle_it 1.779 r_mcangle_other 1.778
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.37 r_dihedral_angle_4_deg 16.039 r_dihedral_angle_3_deg 15.177 r_dihedral_angle_1_deg 8.58 r_lrange_it 4.191 r_lrange_other 4.175 r_scangle_it 2.454 r_scangle_other 2.454 r_mcangle_it 1.779 r_mcangle_other 1.778 r_scbond_it 1.587 r_scbond_other 1.586 r_angle_refined_deg 1.525 r_angle_other_deg 1.258 r_mcbond_it 1.204 r_mcbond_other 1.204 r_symmetry_xyhbond_nbd_refined 0.591 r_symmetry_nbd_refined 0.265 r_nbd_other 0.189 r_nbd_refined 0.188 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.137 r_metal_ion_refined 0.078 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3919 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data reduction PHASER phasing Coot model building Aimless data scaling