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Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT1624-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 20 mg/ml BT1624-S1_15 with 10 mM 6S-GalNAc crystallised in 20 % PEG 6000, 0.2 M ammonium chloride and 0.1 M sodium acetate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.32 47.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.401 α = 90 b = 124.715 β = 95.321 c = 97.137 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 2018-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9790 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 2.7 50.54 100 0.927 3 3.7 56316
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 2.7 2.78 0.662 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6S20 2.7 50.5 56197 2741 99.709 0.23 0.2287 0.2635 0.2718 16.837
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] -1.134 1.09 2.044 -1.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.437 r_dihedral_angle_3_deg 17.453 r_dihedral_angle_4_deg 16.396 r_dihedral_angle_1_deg 6.778 r_lrange_it 2.756 r_lrange_other 2.754 r_angle_refined_deg 1.343 r_mcangle_it 1.247 r_mcangle_other 1.247 r_scangle_it 1.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.437 r_dihedral_angle_3_deg 17.453 r_dihedral_angle_4_deg 16.396 r_dihedral_angle_1_deg 6.778 r_lrange_it 2.756 r_lrange_other 2.754 r_angle_refined_deg 1.343 r_mcangle_it 1.247 r_mcangle_other 1.247 r_scangle_it 1.147 r_scangle_other 1.146 r_angle_other_deg 1.138 r_mcbond_it 0.712 r_mcbond_other 0.712 r_scbond_it 0.647 r_scbond_other 0.647 r_symmetry_xyhbond_nbd_refined 0.24 r_nbd_other 0.222 r_metal_ion_refined 0.199 r_nbd_refined 0.185 r_symmetry_nbd_other 0.181 r_symmetry_nbd_refined 0.18 r_nbtor_refined 0.154 r_xyhbond_nbd_refined 0.151 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_other 0.052 r_chiral_restr 0.051 r_ncsr_local_group_4 0.051 r_ncsr_local_group_6 0.051 r_ncsr_local_group_2 0.05 r_ncsr_local_group_5 0.047 r_ncsr_local_group_1 0.045 r_ncsr_local_group_3 0.044 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14891 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing