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Surface glycan-binding protein B (truncated) from Bacteroides thetaiotaomicron
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295 0.1M magnesium chloride,
0.1M sodium citrate,
15% (w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.21 44.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.689 α = 90 b = 80.689 β = 90 c = 86.027 γ = 90
Symmetry Space Group P 43 21 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 2020-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 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 2.61 19.64 94.5 1 42.5 25.4 8556
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 2.61 2.66 0.951
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 2.611 19.64 8556 414 94.084 0.252 0.2501 0.2503 0.2922 0.2911 53.316
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] 1.844 1.844 -3.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.05 r_dihedral_angle_3_deg 11.941 r_dihedral_angle_4_deg 7.705 r_dihedral_angle_1_deg 6.331 r_angle_other_deg 2.433 r_lrange_it 2.195 r_lrange_other 2.194 r_mcangle_it 1.491 r_mcangle_other 1.491 r_angle_refined_deg 1.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.05 r_dihedral_angle_3_deg 11.941 r_dihedral_angle_4_deg 7.705 r_dihedral_angle_1_deg 6.331 r_angle_other_deg 2.433 r_lrange_it 2.195 r_lrange_other 2.194 r_mcangle_it 1.491 r_mcangle_other 1.491 r_angle_refined_deg 1.181 r_scangle_it 0.908 r_scangle_other 0.907 r_mcbond_it 0.807 r_mcbond_other 0.806 r_scbond_it 0.478 r_scbond_other 0.477 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.154 r_nbd_refined 0.145 r_nbd_other 0.141 r_xyhbond_nbd_refined 0.128 r_symmetry_xyhbond_nbd_other 0.122 r_symmetry_nbd_refined 0.12 r_symmetry_nbtor_other 0.064 r_symmetry_xyhbond_nbd_refined 0.038 r_bond_other_d 0.037 r_chiral_restr 0.025 r_gen_planes_refined 0.002 r_gen_planes_other 0.002 r_bond_refined_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1861 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing