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Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin E190D mutant in complex with 6'-SLN
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, 6% PEG 8000, and 39% 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.93 58.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.784 α = 90 b = 130.842 β = 97.9 c = 72.179 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 PILATUS3 6M 2016-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0331 APS 23-ID-D
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 99.8 0.08 0.04 1 15.7 6.5 91326 34
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 2.32 98.2 0.59 0.3 0.74 1.5 4.5
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 86754 4571 99.22 0.17917 0.17768 0.1823 0.20787 0.2108 RANDOM 49.477
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] 0.62 0.34 -1.07 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.897 r_dihedral_angle_4_deg 15.474 r_dihedral_angle_3_deg 14.092 r_dihedral_angle_1_deg 6.005 r_long_range_B_refined 5.604 r_long_range_B_other 5.527 r_scangle_other 2.484 r_angle_refined_deg 1.469 r_scbond_it 1.432 r_scbond_other 1.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.897 r_dihedral_angle_4_deg 15.474 r_dihedral_angle_3_deg 14.092 r_dihedral_angle_1_deg 6.005 r_long_range_B_refined 5.604 r_long_range_B_other 5.527 r_scangle_other 2.484 r_angle_refined_deg 1.469 r_scbond_it 1.432 r_scbond_other 1.431 r_mcangle_it 1.319 r_mcangle_other 1.319 r_angle_other_deg 0.946 r_mcbond_it 0.74 r_mcbond_other 0.735 r_chiral_restr 0.11 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 805 Heterogen Atoms 486
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling PHASER phasing