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Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT4631_S1_15)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OZE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 80 mg/ml BT4631 with 10 mM 6S-Gal was crystallised in 20 % PEG 10K and 0.1 M Bicine pH8.5.
Crystal Properties Matthews coefficient Solvent content 2.81 56.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.924 α = 90 b = 109.572 β = 90 c = 117.531 γ = 90
Symmetry Space Group P 2 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 EIGER X 16M 2020-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 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 1.35 109.57 98.8 0.999 25.4 12.4 140145
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 1.35 1.37 0.955 4.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7OZE 1.35 80.274 140055 7206 98.612 0.124 0.1233 0.1229 0.1391 0.1386 14.129
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] 0.928 -0.247 -0.681
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.774 r_dihedral_angle_4_deg 20.393 r_dihedral_angle_3_deg 12.543 r_dihedral_angle_1_deg 6.869 r_lrange_it 2.719 r_lrange_other 2.213 r_scangle_it 1.639 r_scangle_other 1.639 r_angle_refined_deg 1.482 r_angle_other_deg 1.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.774 r_dihedral_angle_4_deg 20.393 r_dihedral_angle_3_deg 12.543 r_dihedral_angle_1_deg 6.869 r_lrange_it 2.719 r_lrange_other 2.213 r_scangle_it 1.639 r_scangle_other 1.639 r_angle_refined_deg 1.482 r_angle_other_deg 1.474 r_scbond_it 1.374 r_scbond_other 1.374 r_rigid_bond_restr 1.202 r_mcangle_it 1.176 r_mcangle_other 1.175 r_mcbond_it 0.981 r_mcbond_other 0.931 r_symmetry_nbd_refined 0.428 r_nbd_other 0.302 r_nbd_refined 0.238 r_symmetry_xyhbond_nbd_refined 0.19 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.139 r_metal_ion_refined 0.111 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.078 r_symmetry_xyhbond_nbd_other 0.014 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 3780 Nucleic Acid Atoms Solvent Atoms 599 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing