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Structure of SigLec-10 in complex with 2,6-Sialyllactose
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 293.15 0.085 M Sodium Citrate pH 5.1, 0.17 M Ammonium Acetate, 15% v/v Glycerol, and 29% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.27 62.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.188 α = 90 b = 83.188 β = 90 c = 484.668 γ = 120
Symmetry Space Group P 65 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 EIGER X 16M 2024-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.97946 SSRL BL12-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.7 48.11 99.8 0.192 0.199 0.049 0.996 12.6 16.6 28605
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 98.7 0.59 0.612 0.16 0.84 13.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.7 39.37 27085 1444 99.56 0.22356 0.22079 0.23 0.27626 0.2784 RANDOM 78.497
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] 2.02 1.01 2.02 -6.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.195 r_long_range_B_refined 15.692 r_mcangle_it 9.889 r_scbond_it 8.42 r_dihedral_angle_1_deg 7.026 r_mcbond_it 6.725 r_dihedral_angle_2_deg 5.793 r_angle_refined_deg 1.763 r_chiral_restr 0.155 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.195 r_long_range_B_refined 15.692 r_mcangle_it 9.889 r_scbond_it 8.42 r_dihedral_angle_1_deg 7.026 r_mcbond_it 6.725 r_dihedral_angle_2_deg 5.793 r_angle_refined_deg 1.763 r_chiral_restr 0.155 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5206 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing