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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 293.15 450 mM sodium malonate pH 7.0, 24% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.23 61.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.724 α = 90 b = 82.724 β = 90 c = 121.682 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 2.1 82.72 99.7 0.996 8.7 6.8 47588
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 2.1 2.16 0.557 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 2.1 82.72 47526 2369 99.619 0.187 0.1856 0.1933 0.2109 0.2138 36.817
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] -0.251 -0.251 0.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.913 r_dihedral_angle_4_deg 16.089 r_dihedral_angle_3_deg 15.394 r_dihedral_angle_1_deg 8.712 r_lrange_it 4.295 r_lrange_other 4.29 r_scangle_it 2.659 r_scangle_other 2.659 r_mcangle_it 1.878 r_mcangle_other 1.878
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.913 r_dihedral_angle_4_deg 16.089 r_dihedral_angle_3_deg 15.394 r_dihedral_angle_1_deg 8.712 r_lrange_it 4.295 r_lrange_other 4.29 r_scangle_it 2.659 r_scangle_other 2.659 r_mcangle_it 1.878 r_mcangle_other 1.878 r_scbond_it 1.681 r_scbond_other 1.681 r_angle_refined_deg 1.589 r_angle_other_deg 1.287 r_mcbond_it 1.202 r_mcbond_other 1.2 r_symmetry_xyhbond_nbd_refined 0.389 r_symmetry_nbd_refined 0.224 r_nbd_other 0.203 r_nbd_refined 0.192 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.149 r_metal_ion_refined 0.102 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.049 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 142 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data reduction PHASER phasing Coot model building Aimless data scaling