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Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin HA2 I45T 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 58.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.212 α = 90 b = 131.146 β = 98.15 c = 72.176 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 2.25 50 97.4 0.09 0.04 1 16.2 5 89621 38
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 2.25 2.35 95.7 0.94 0.49 0.68 1.3 4.7
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 2.25 50 84488 4390 97.36 0.18313 0.18186 0.1861 0.20759 0.211 RANDOM 50.917
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] 1.33 0.56 -0.7 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.598 r_dihedral_angle_4_deg 17.134 r_dihedral_angle_3_deg 14.503 r_dihedral_angle_1_deg 6.101 r_long_range_B_refined 5.54 r_long_range_B_other 5.492 r_scangle_other 3.077 r_mcangle_it 1.845 r_mcangle_other 1.845 r_scbond_it 1.793
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.598 r_dihedral_angle_4_deg 17.134 r_dihedral_angle_3_deg 14.503 r_dihedral_angle_1_deg 6.101 r_long_range_B_refined 5.54 r_long_range_B_other 5.492 r_scangle_other 3.077 r_mcangle_it 1.845 r_mcangle_other 1.845 r_scbond_it 1.793 r_scbond_other 1.793 r_angle_refined_deg 1.545 r_mcbond_it 1.118 r_mcbond_other 1.118 r_angle_other_deg 0.958 r_chiral_restr 0.085 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 11517 Nucleic Acid Atoms Solvent Atoms 666 Heterogen Atoms 332
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing