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GspB Siglec domain bound to sialyl T antigen linked to serine-FMOC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 1 uL protein (22 mg/ml preincubated in 10 mM sTa-Ser-FMOC) and 2 uL reservoir solution over 600 uL reservoir solution ( 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5, 50% PEG 4000). Crystals were cryoprotected in 25% (v/v) glycerol and flash-cooled in liquid nitrogen. protein was in 18 mM Tris-HCl, pH 7.5, and 200 mM NaCl.
Crystal Properties Matthews coefficient Solvent content 1.96 37.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.987 α = 70.2 b = 38.111 β = 68.01 c = 47.054 γ = 62.08
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 PILATUS 6M 2023-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM07 0.97951 ESRF BM07
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.89 23.1 86 0.184 0.065 0.999 26.2 3.1 14353 23.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.93 63.2 0.218 0.981
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.89 23.1 2.05 14353 711 84.65 0.1851 0.1837 0.1839 0.2109 0.2143 40.12
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 13.539 f_angle_d 0.7394 f_chiral_restr 0.0545 f_bond_d 0.0051 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1927 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 152
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing