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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 (BT4683-S1_4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HDH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 20 % PEG 3350, 0.2 M sodium iodide and BTP pH 8.5
25mg/ml
Crystal Properties Matthews coefficient Solvent content 2.07 40.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.136 α = 90 b = 87.799 β = 90 c = 101.833 γ = 90
Symmetry Space Group P 21 21 21
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 X 16M 2019-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 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 1.63 66.585 99.9 0.999 7.8 1.9 62376
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 1.63 1.66 0.795 1.4
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 1HDH 1.63 66.585 62376 3095 99.896 0.175 0.174 0.1835 0.2003 0.2101 22.124
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] -1.456 -1.189 2.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.3 r_dihedral_angle_4_deg 18.507 r_dihedral_angle_3_deg 14.339 r_dihedral_angle_1_deg 6.977 r_lrange_it 4.733 r_lrange_other 4.665 r_scangle_it 3.921 r_scangle_other 3.92 r_scbond_it 2.555 r_scbond_other 2.554
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.3 r_dihedral_angle_4_deg 18.507 r_dihedral_angle_3_deg 14.339 r_dihedral_angle_1_deg 6.977 r_lrange_it 4.733 r_lrange_other 4.665 r_scangle_it 3.921 r_scangle_other 3.92 r_scbond_it 2.555 r_scbond_other 2.554 r_mcangle_other 2.146 r_mcangle_it 2.142 r_angle_refined_deg 1.53 r_mcbond_it 1.518 r_mcbond_other 1.504 r_angle_other_deg 1.389 r_metal_ion_refined 0.251 r_nbd_refined 0.203 r_nbd_other 0.202 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.172 r_symmetry_nbd_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.077 r_symmetry_nbtor_other 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3991 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling BALBES phasing