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Surface glycan-binding protein B from Bacteroides fluxus in complex with mixed-linkage glucotriose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295 0.1 M MES pH6.6,
0.2 M ammonium sulfate,
20 % (w/v) PEG5000MME,
0.1M guanidine hydrochloride
Crystal Properties Matthews coefficient Solvent content 2.75 55.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.98 α = 90 b = 77.222 β = 90 c = 148.379 γ = 90
Symmetry Space Group I 2 2 2
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 PILATUS3 6M 2020-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
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 1.6 74.19 95.5 0.999 34.4 11.8 43047
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 1.61 1.64 0.907
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 1.6 74.189 43047 2197 95.437 0.18 0.1782 0.1782 0.2043 0.2039 31.631
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] -0.937 3.521 -2.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.727 r_dihedral_angle_4_deg 19.674 r_dihedral_angle_3_deg 11.218 r_dihedral_angle_1_deg 7.333 r_lrange_it 6.521 r_lrange_other 6.294 r_scangle_it 5.235 r_scangle_other 5.233 r_scbond_it 3.776 r_scbond_other 3.775
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.727 r_dihedral_angle_4_deg 19.674 r_dihedral_angle_3_deg 11.218 r_dihedral_angle_1_deg 7.333 r_lrange_it 6.521 r_lrange_other 6.294 r_scangle_it 5.235 r_scangle_other 5.233 r_scbond_it 3.776 r_scbond_other 3.775 r_mcangle_other 3.264 r_mcangle_it 3.254 r_mcbond_it 2.588 r_mcbond_other 2.559 r_angle_other_deg 2.464 r_angle_refined_deg 1.729 r_symmetry_nbd_other 0.221 r_nbd_refined 0.203 r_nbd_other 0.192 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.168 r_symmetry_nbd_refined 0.164 r_symmetry_xyhbond_nbd_other 0.155 r_symmetry_xyhbond_nbd_refined 0.12 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.083 r_bond_other_d 0.037 r_dihedral_angle_other_2_deg 0.028 r_gen_planes_other 0.014 r_bond_refined_d 0.012 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1907 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing