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Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3057-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 295 35 mg/ml BT3057S1_16 with 10 mM 4S-GalNAc was crystallised in 20 % PEG 3350 and 0.2 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2.45 49.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.17 α = 90 b = 90.755 β = 98.55 c = 94.169 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 1.907 65.52 99.6 0.992 8.8 1.9 85409
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 1.91 1.94 0.39 2.2
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 7AN1 1.907 65.52 85408 4097 99.594 0.187 0.1849 0.1953 0.2233 0.2307 23.895
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] 0.256 -0.004 0.587 -0.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.528 r_dihedral_angle_4_deg 14.651 r_dihedral_angle_3_deg 14.12 r_dihedral_angle_1_deg 7.14 r_lrange_it 4.169 r_lrange_other 4.13 r_scangle_it 2.996 r_scangle_other 2.996 r_mcangle_it 2.35 r_mcangle_other 2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.528 r_dihedral_angle_4_deg 14.651 r_dihedral_angle_3_deg 14.12 r_dihedral_angle_1_deg 7.14 r_lrange_it 4.169 r_lrange_other 4.13 r_scangle_it 2.996 r_scangle_other 2.996 r_mcangle_it 2.35 r_mcangle_other 2.35 r_scbond_it 1.938 r_scbond_other 1.938 r_mcbond_it 1.622 r_mcbond_other 1.621 r_angle_refined_deg 1.478 r_angle_other_deg 1.281 r_nbd_refined 0.195 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.157 r_metal_ion_refined 0.145 r_nbd_other 0.142 r_symmetry_nbd_refined 0.114 r_symmetry_xyhbond_nbd_other 0.093 r_symmetry_xyhbond_nbd_refined 0.087 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.069 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 7540 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing