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Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3796_S1_16)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20 mg/ml BT3796S1_16 with 10mM 4S-GalNAc was crystallised in 20 % PEG 6000, 0.2 M magnesium chloride and 0.1 MES pH 6.0.
Crystal Properties Matthews coefficient Solvent content 2.26 45.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.18 α = 90 b = 88.95 β = 112.05 c = 87.91 γ = 90
Symmetry Space Group P 1 21 1
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-F 2018-07-18 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 1.5 81.613 99.7 0.996 7 1.9 166081
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 1.5 1.53 0.577 1.5
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 7AN1 1.5 81.613 165846 8251 99.473 0.143 0.1415 0.1757 0.1884 17.155
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] -0.453 -0.318 2.979 -1.708
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.758 r_dihedral_angle_4_deg 15.235 r_dihedral_angle_3_deg 11.701 r_rigid_bond_restr 8.597 r_dihedral_angle_1_deg 6.621 r_lrange_it 3.083 r_lrange_other 2.881 r_scangle_other 2.759 r_scangle_it 2.758 r_scbond_other 2.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.758 r_dihedral_angle_4_deg 15.235 r_dihedral_angle_3_deg 11.701 r_rigid_bond_restr 8.597 r_dihedral_angle_1_deg 6.621 r_lrange_it 3.083 r_lrange_other 2.881 r_scangle_other 2.759 r_scangle_it 2.758 r_scbond_other 2.291 r_scbond_it 2.29 r_mcangle_it 2.183 r_mcangle_other 2.183 r_mcbond_it 1.753 r_mcbond_other 1.745 r_angle_refined_deg 1.477 r_angle_other_deg 1.409 r_nbd_other 0.22 r_symmetry_nbd_refined 0.213 r_nbd_refined 0.199 r_symmetry_nbd_other 0.183 r_symmetry_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.168 r_metal_ion_refined 0.123 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.077 r_ncsr_local_group_1 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7625 Nucleic Acid Atoms Solvent Atoms 755 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing