☰ Navigation Tabs
Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3109_S1_15)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S20
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10 mg/ml of BT3109S1_15 with 10 mM 6S-Gal was crystallised in 30 % PEG 4000, 0.2 M ammonium acetate and sodium citrate pH 5.6.
Crystal Properties Matthews coefficient Solvent content 1.97 37.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.15 α = 90 b = 91.76 β = 116.63 c = 52.68 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 EIGER2 X 16M 2019-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 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 1.75 47.136 99.5 0.997 8.8 3.5 44392
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 1.75 1.78 0.493 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 FREE R-VALUE 6S20 1.75 47.09 44366 2071 99.308 0.185 0.1836 0.1919 0.217 0.2241 27.325
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] -2.142 0.242 0.213 1.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.428 r_dihedral_angle_4_deg 15.537 r_dihedral_angle_3_deg 14.505 r_dihedral_angle_1_deg 7.113 r_lrange_it 4.721 r_lrange_other 4.711 r_scangle_other 3.704 r_scangle_it 3.703 r_mcangle_it 2.496 r_mcangle_other 2.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.428 r_dihedral_angle_4_deg 15.537 r_dihedral_angle_3_deg 14.505 r_dihedral_angle_1_deg 7.113 r_lrange_it 4.721 r_lrange_other 4.711 r_scangle_other 3.704 r_scangle_it 3.703 r_mcangle_it 2.496 r_mcangle_other 2.496 r_scbond_other 2.417 r_scbond_it 2.415 r_mcbond_it 1.854 r_mcbond_other 1.853 r_angle_refined_deg 1.492 r_angle_other_deg 1.317 r_symmetry_xyhbond_nbd_other 0.567 r_symmetry_xyhbond_nbd_refined 0.212 r_nbd_refined 0.203 r_symmetry_nbd_other 0.179 r_xyhbond_nbd_refined 0.17 r_nbd_other 0.167 r_nbtor_refined 0.162 r_metal_ion_refined 0.101 r_symmetry_nbd_refined 0.094 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.066 r_xyhbond_nbd_other 0.012 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3731 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing