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Structure of Hemagglutinin from Influenza A/Victoria/22/2020
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291.15 50% PEG-200, 0.1M citrate pH 5.5, final pH 6.9
Crystal Properties Matthews coefficient Solvent content 3.39 63.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.705 α = 90 b = 99.705 β = 90 c = 395.31 γ = 120
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 9M 2021-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12723 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.035 79.252 98.6 0.077 0.079 0.999 21.6 20.4 48446
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.035 2.071 98 1.642 0.865 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 NONE 2YP4 2.035 79.252 48446 2400 98.556 0.204 0.2028 0.2028 0.2291 0.2289 54.981
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] -0.005 -0.003 -0.005 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.247 r_dihedral_angle_3_deg 15.356 r_dihedral_angle_4_deg 14.224 r_lrange_it 8.29 r_scangle_it 6.968 r_dihedral_angle_1_deg 6.933 r_scbond_it 5.072 r_mcangle_it 4.935 r_mcbond_it 3.901 r_angle_refined_deg 1.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.247 r_dihedral_angle_3_deg 15.356 r_dihedral_angle_4_deg 14.224 r_lrange_it 8.29 r_scangle_it 6.968 r_dihedral_angle_1_deg 6.933 r_scbond_it 5.072 r_mcangle_it 4.935 r_mcbond_it 3.901 r_angle_refined_deg 1.473 r_nbtor_refined 0.313 r_nbd_refined 0.215 r_symmetry_nbd_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.15 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.103 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3941 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction XDS data scaling PHENIX phasing