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Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3177_S1_11)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G2V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20 mg/ml BT3177S1_11 with 10 mM 6S-GlcNAc crystallised in 50 % precipitant mix 1 (40% v/v PEG 500, MME; 20 % w/v PEG 20000), 0.1 M carboxcylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate) and 0.1 M buffer system 3 pH 8.5 (Tris (base); BICINE).
Crystal Properties Matthews coefficient Solvent content 2.3 46.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.129 α = 90 b = 69.78 β = 97.644 c = 96.286 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 0.97 35.856 91.9 0.996 8.8 1.9 298423
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 0.97 0.99 0.596 1.5
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 5G2V 0.97 35.856 298370 14930 91.71 0.124 0.1236 0.1228 0.1362 0.1354 11.374
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] 1.281 0.725 0.419 -1.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.367 r_dihedral_angle_4_deg 12.923 r_dihedral_angle_3_deg 12.367 r_dihedral_angle_1_deg 7.221 r_rigid_bond_restr 3.1 r_lrange_it 2.135 r_lrange_other 1.753 r_angle_other_deg 1.503 r_angle_refined_deg 1.502 r_scangle_other 1.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.367 r_dihedral_angle_4_deg 12.923 r_dihedral_angle_3_deg 12.367 r_dihedral_angle_1_deg 7.221 r_rigid_bond_restr 3.1 r_lrange_it 2.135 r_lrange_other 1.753 r_angle_other_deg 1.503 r_angle_refined_deg 1.502 r_scangle_other 1.142 r_scangle_it 1.141 r_mcangle_it 1.02 r_mcangle_other 1.02 r_scbond_other 0.892 r_scbond_it 0.891 r_mcbond_it 0.791 r_mcbond_other 0.788 r_nbd_refined 0.247 r_nbd_other 0.22 r_symmetry_nbd_refined 0.199 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.129 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.074 r_metal_ion_refined 0.048 r_gen_planes_refined 0.009 r_bond_refined_d 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 4110 Nucleic Acid Atoms Solvent Atoms 593 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing