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Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin HA2 I45F 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 2.94 58.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.378 α = 90 b = 131.409 β = 98.07 c = 72.28 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 2.1 50 97.4 0.1 0.05 1 20 5.6 110282
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 2.1 2.2 98.1 0.83 0.4 0.77 1.7 5.2
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 (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 2.1 50 103850 5420 97.38 0.18588 0.18432 0.1912 0.21614 0.2238 RANDOM 48.81
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] 1.09 0.87 0.32 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.284 r_dihedral_angle_4_deg 16.414 r_dihedral_angle_3_deg 14.553 r_dihedral_angle_1_deg 5.951 r_long_range_B_refined 5.423 r_long_range_B_other 5.326 r_scangle_other 2.75 r_scbond_it 1.618 r_scbond_other 1.618 r_mcangle_it 1.614
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.284 r_dihedral_angle_4_deg 16.414 r_dihedral_angle_3_deg 14.553 r_dihedral_angle_1_deg 5.951 r_long_range_B_refined 5.423 r_long_range_B_other 5.326 r_scangle_other 2.75 r_scbond_it 1.618 r_scbond_other 1.618 r_mcangle_it 1.614 r_mcangle_other 1.613 r_angle_refined_deg 1.497 r_mcbond_it 0.994 r_mcbond_other 0.994 r_angle_other_deg 0.941 r_chiral_restr 0.086 r_bond_refined_d 0.011 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 11529 Nucleic Acid Atoms Solvent Atoms 846 Heterogen Atoms 332
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing