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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 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.23 61.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.918 α = 90 b = 82.918 β = 90 c = 121.31 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 2018-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9793 Diamond I03
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 19.99 99.2 0.999 14 7.6 55261
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 2.05 0.472 1.2
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 THROUGHOUT 3ILN 2 19.99 55218 2638 99.873 0.188 0.1867 0.1948 0.2108 0.219 43.976
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] -0.615 -0.615 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.438 r_dihedral_angle_4_deg 19.296 r_dihedral_angle_3_deg 15.078 r_dihedral_angle_1_deg 8.547 r_lrange_it 5.217 r_lrange_other 5.213 r_scangle_it 2.937 r_scangle_other 2.937 r_mcangle_it 2.169 r_mcangle_other 2.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.438 r_dihedral_angle_4_deg 19.296 r_dihedral_angle_3_deg 15.078 r_dihedral_angle_1_deg 8.547 r_lrange_it 5.217 r_lrange_other 5.213 r_scangle_it 2.937 r_scangle_other 2.937 r_mcangle_it 2.169 r_mcangle_other 2.168 r_scbond_it 1.898 r_scbond_other 1.898 r_angle_refined_deg 1.626 r_mcbond_it 1.448 r_mcbond_other 1.448 r_angle_other_deg 1.29 r_symmetry_xyhbond_nbd_refined 0.57 r_symmetry_nbd_refined 0.227 r_nbd_refined 0.222 r_symmetry_nbd_other 0.189 r_nbd_other 0.181 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.141 r_metal_ion_refined 0.124 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.072 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 99 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building