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A single sulfatase is required for metabolism of colonic mucin O-glycans and intestinal colonization by a symbiotic human gut bacterium (BT1622-S1_20)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other BT1624
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 20 % PEG 3350, 0.2 M Sodium citrate,
25 mg/ml BT1622 and 10 mM LacNAc.
Crystal Properties Matthews coefficient Solvent content 2.79 55.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.268 α = 90 b = 81.268 β = 90 c = 383.735 γ = 90
Symmetry Space Group P 43 21 2
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 XE 16M 2018-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9790 Diamond I04
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 2.6 96.118 97.8 0.987 5.5 7.3 40144
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 2.6 2.71 0.344
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE BT1624 2.6 95.93 40015 1975 97.614 0.22 0.2187 0.2448 0.2316 57.279
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] 0.003 0.003 -0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.258 r_dihedral_angle_4_deg 19.037 r_dihedral_angle_3_deg 15.265 r_dihedral_angle_1_deg 7.398 r_lrange_it 1.879 r_lrange_other 1.875 r_angle_refined_deg 1.319 r_angle_other_deg 1.129 r_mcangle_it 0.672 r_mcangle_other 0.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.258 r_dihedral_angle_4_deg 19.037 r_dihedral_angle_3_deg 15.265 r_dihedral_angle_1_deg 7.398 r_lrange_it 1.879 r_lrange_other 1.875 r_angle_refined_deg 1.319 r_angle_other_deg 1.129 r_mcangle_it 0.672 r_mcangle_other 0.672 r_scangle_it 0.572 r_scangle_other 0.572 r_mcbond_it 0.379 r_mcbond_other 0.379 r_scbond_it 0.32 r_scbond_other 0.32 r_nbd_refined 0.189 r_metal_ion_refined 0.179 r_symmetry_nbd_other 0.176 r_nbd_other 0.171 r_nbtor_refined 0.164 r_symmetry_nbd_refined 0.155 r_xyhbond_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.126 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.054 r_ncsr_local_group_1 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7570 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing