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Surface glycan-binding protein B from Bacteroides fluxus
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 2.72 54.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.533 α = 90 b = 77.619 β = 90 c = 146.621 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 BL9-2 0.97946 SSRL BL9-2
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 1.82 39.71 99.7 0.999 12.3 6.6 30831
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 1.82 1.86 0.934
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 1.82 39.709 30831 1532 99.683 0.193 0.1909 0.191 0.2301 0.2301 31.74
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] -1.527 5.096 -3.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.022 r_dihedral_angle_4_deg 17.565 r_dihedral_angle_3_deg 11.623 r_dihedral_angle_1_deg 7.558 r_lrange_it 5.876 r_lrange_other 5.875 r_scangle_it 4.559 r_scangle_other 4.557 r_scbond_it 3.283 r_scbond_other 3.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.022 r_dihedral_angle_4_deg 17.565 r_dihedral_angle_3_deg 11.623 r_dihedral_angle_1_deg 7.558 r_lrange_it 5.876 r_lrange_other 5.875 r_scangle_it 4.559 r_scangle_other 4.557 r_scbond_it 3.283 r_scbond_other 3.281 r_mcangle_other 3.251 r_mcangle_it 3.25 r_mcbond_it 2.445 r_angle_other_deg 2.443 r_mcbond_other 2.44 r_angle_refined_deg 1.555 r_symmetry_xyhbond_nbd_refined 0.219 r_symmetry_nbd_other 0.216 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.172 r_nbd_other 0.161 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.069 r_symmetry_nbd_refined 0.065 r_bond_other_d 0.037 r_dihedral_angle_other_2_deg 0.026 r_gen_planes_other 0.011 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_symmetry_xyhbond_nbd_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1851 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing