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Surface glycan-binding protein B from Bacteroides fluxus in complex with laminaritriose
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,
0.1 M guanidine hydrochloride
Crystal Properties Matthews coefficient Solvent content 2.55 51.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.268 α = 90 b = 59.249 β = 102.611 c = 148.137 γ = 90
Symmetry Space Group I 1 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 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 1.76 37.38 93.5 0.999 21.6 6.8 57885
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 1.76 1.79 0.972
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 1.76 35.664 57885 2864 92.663 0.161 0.1591 0.1592 0.2018 0.2019 24.287
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] 2.047 1.322 -1.262 -1.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.853 r_dihedral_angle_4_deg 16.691 r_dihedral_angle_3_deg 11.518 r_lrange_it 7.956 r_dihedral_angle_1_deg 7.36 r_lrange_other 6.757 r_scangle_it 4.298 r_scangle_other 4.27 r_scbond_it 2.943 r_scbond_other 2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.853 r_dihedral_angle_4_deg 16.691 r_dihedral_angle_3_deg 11.518 r_lrange_it 7.956 r_dihedral_angle_1_deg 7.36 r_lrange_other 6.757 r_scangle_it 4.298 r_scangle_other 4.27 r_scbond_it 2.943 r_scbond_other 2.9 r_mcangle_other 2.63 r_mcangle_it 2.629 r_angle_other_deg 2.518 r_mcbond_it 2.016 r_mcbond_other 2.013 r_angle_refined_deg 1.642 r_symmetry_xyhbond_nbd_refined 0.305 r_symmetry_nbd_refined 0.248 r_nbd_refined 0.237 r_symmetry_nbd_other 0.223 r_xyhbond_nbd_refined 0.196 r_nbd_other 0.185 r_nbtor_refined 0.172 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.075 r_bond_other_d 0.037 r_gen_planes_other 0.019 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3824 Nucleic Acid Atoms Solvent Atoms 645 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing