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Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin HA2 I45M mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FNK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 38% 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.07 40.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.856 α = 90 b = 131.006 β = 98.4 c = 72.576 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M 2018-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
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 2.5 50 97.6 0.12 0.05 1 15.4 5.9 65790 48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 98.4 0.87 0.39 0.7 1.5 5.9
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 (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 4FNK 2.5 50 61835 3292 97.5 0.19179 0.19035 0.1922 0.21888 0.221 RANDOM 57.018
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] 1.08 -0.83 -3.21 2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.323 r_dihedral_angle_4_deg 15.931 r_dihedral_angle_3_deg 14.952 r_dihedral_angle_1_deg 6.16 r_long_range_B_refined 5.34 r_long_range_B_other 5.33 r_scangle_other 2.867 r_mcangle_it 1.871 r_mcangle_other 1.871 r_scbond_it 1.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.323 r_dihedral_angle_4_deg 15.931 r_dihedral_angle_3_deg 14.952 r_dihedral_angle_1_deg 6.16 r_long_range_B_refined 5.34 r_long_range_B_other 5.33 r_scangle_other 2.867 r_mcangle_it 1.871 r_mcangle_other 1.871 r_scbond_it 1.652 r_scbond_other 1.652 r_angle_refined_deg 1.522 r_mcbond_it 1.098 r_mcbond_other 1.096 r_angle_other_deg 0.947 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11520 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 318
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing REFMAC refinement