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Crystal Structure Analysis of Polyporus squamosus lectin bound to human-type influenza-binding epitope Neu5Aca2-6Galb1-4GlcNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IHO PDB entry 2IHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 7 293 PEG 8000, pH 7, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.84 56.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.809 α = 90 b = 59.4 β = 90 c = 103.228 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 210 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.7 38.5 99 0.06 26.3 5.8 79179 78403 2 2 28.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 92.8 0.238 2.68
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 2IHO 1.7 38.5 79179 78403 3939 99.02 0.1867 0.1851 0.1872 0.217 0.219 RANDOM 28.8929
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 r_dihedral_angle_2_deg 34.943 r_dihedral_angle_4_deg 23.103 r_dihedral_angle_3_deg 12.441 r_dihedral_angle_1_deg 7.396 r_scangle_it 4.558 r_scbond_it 3.032 r_mcangle_it 2.349 r_angle_refined_deg 1.981 r_mcbond_it 1.388 r_chiral_restr 0.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.943 r_dihedral_angle_4_deg 23.103 r_dihedral_angle_3_deg 12.441 r_dihedral_angle_1_deg 7.396 r_scangle_it 4.558 r_scbond_it 3.032 r_mcangle_it 2.349 r_angle_refined_deg 1.981 r_mcbond_it 1.388 r_chiral_restr 0.151 r_bond_refined_d 0.023 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4318 Nucleic Acid Atoms Solvent Atoms 632 Heterogen Atoms 92
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction