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Crystal structure of H5 hemagglutinin from swan-infecting H5N8 influenza virus in complex with LSTa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K65
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 3 % dextran sulfate sodium salt, 0.1 M bicine pH 8.5, 19 % (w/v) PEG20000
Crystal Properties Matthews coefficient Solvent content 3.3 62.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.151 α = 90 b = 108.495 β = 99.789 c = 133.192 γ = 90
Symmetry Space Group P 1 21 1
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 2021-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979183 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.6 50 98.1 0.167 9.291 4.3 66519 36.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 1.074
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.613 26.328 63213 1903 92.658 0.186 0.1841 0.1885 0.2306 0.2258 36.264
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] 1.859 -2.837 0.938 -1.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.527 r_dihedral_angle_6_deg 14.762 r_lrange_it 10.019 r_lrange_other 10.01 r_dihedral_angle_2_deg 9.297 r_scangle_it 7.627 r_scangle_other 7.626 r_dihedral_angle_1_deg 7.348 r_mcangle_it 5.673 r_mcangle_other 5.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.527 r_dihedral_angle_6_deg 14.762 r_lrange_it 10.019 r_lrange_other 10.01 r_dihedral_angle_2_deg 9.297 r_scangle_it 7.627 r_scangle_other 7.626 r_dihedral_angle_1_deg 7.348 r_mcangle_it 5.673 r_mcangle_other 5.673 r_scbond_it 4.719 r_scbond_other 4.719 r_mcbond_it 3.564 r_mcbond_other 3.564 r_angle_refined_deg 1.826 r_angle_other_deg 0.626 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.22 r_symmetry_nbd_other 0.204 r_nbd_other 0.201 r_nbtor_refined 0.187 r_symmetry_nbd_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_other 0.102 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11784 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing