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Hsa Siglec and Unique domains in complex with 3'sialyl-N-acetyllactosamine trisaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EFC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 21.6 mg/mL protein in 20 mM Tris-HCl, pH 7.2
sitting drop vapor diffusion
drops contain 1uL protein solution and 2uL reservoir solution.
Reservoir solution: 0.1 M Succinate/Phosphate/Glycine pH 10.0 and 25% PEG 3350.
Crystals were soaked with 5mM ligand for 20 hours, no cryoprotection was used beyond the reservoir buffer
Crystal Properties Matthews coefficient Solvent content 1.94 36.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.743 α = 90 b = 57.738 β = 90 c = 75.86 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 PILATUS3 6M 2019-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rpim I (All) 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 2.15 50 99.6 0.126 0.055 0.993 12.1 4.6 10881 34.14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 0.643 0.283
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6EFC 2.15 32.42 1.34 10845 313 93.57 0.2068 0.206 0.208 0.2333 0.2521 44.6
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 16.8283 f_angle_d 2.3525 f_chiral_restr 0.1472 f_bond_d 0.0235 f_plane_restr 0.0151
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1584 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 48
Software Software Software Name Purpose Coot model building PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing