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Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT1918_S1_46)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VQR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 20 mg/ml of BT1918S1_46 with 10 mM 6S-GlcNAc was crystallised in 45 % MPD, 0.2 M CaCl2 and 0.1 M Bis-Tris pH 5.5.
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.389 α = 90 b = 56.389 β = 90 c = 279.763 γ = 120
Symmetry Space Group P 32 2 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 2018-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979 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 1.95 48.153 100 0.99 5.8 10.3 39105
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 1.95 2 0.803
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 2vqr 1.95 48.153 39003 2032 99.936 0.189 0.1882 0.1968 0.2037 0.2094 29.506
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] 0.93 0.465 0.93 -3.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.572 r_dihedral_angle_4_deg 15.241 r_dihedral_angle_3_deg 12.875 r_dihedral_angle_1_deg 7.082 r_lrange_it 4.847 r_lrange_other 4.842 r_scangle_it 3.825 r_scangle_other 3.825 r_mcangle_it 2.895 r_mcangle_other 2.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.572 r_dihedral_angle_4_deg 15.241 r_dihedral_angle_3_deg 12.875 r_dihedral_angle_1_deg 7.082 r_lrange_it 4.847 r_lrange_other 4.842 r_scangle_it 3.825 r_scangle_other 3.825 r_mcangle_it 2.895 r_mcangle_other 2.895 r_scbond_it 2.515 r_scbond_other 2.515 r_mcbond_it 2.11 r_mcbond_other 2.11 r_angle_refined_deg 1.511 r_angle_other_deg 1.321 r_nbd_refined 0.206 r_nbd_other 0.205 r_symmetry_nbd_other 0.189 r_symmetry_nbd_refined 0.189 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.161 r_xyhbond_nbd_refined 0.133 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3787 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing