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Surface glycan-binding protein A (SGBP-A, SusD-like) from a mixed-linkage beta-glucan utilization locus in Segatella copri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Tris-HCl (pH 8.5) and 26% (w/v) Polyethylene glycol (PEG) 8,000
Crystal Properties Matthews coefficient Solvent content 1.97 37.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.877 α = 90 b = 76.849 β = 90 c = 99.918 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2022-05-23 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) R Merge I (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 2.05 33.56 99.31 0.0449 0.998 8.41 2 33784 27.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.123 0.2893 0.958 2.24
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.05 33.56 1.34 33784 2558 98.94 0.1872 0.1853 0.2331 0.25 30.15
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.7767 f_angle_d 0.8477 f_chiral_restr 0.0464 f_plane_restr 0.0081 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4296 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing