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Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin G225Q/L226A mutant apo form
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 2.96 58.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.735 α = 90 b = 131.202 β = 98.35 c = 72.439 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 2016-10-15 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 2.15 50 99.6 0.08 0.03 1 20.1 6.2 105027
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 2.15 2.22 97.5 0.57 0.27 0.82 1.9 4.8
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 2.15 50 99672 5341 99.42 0.17686 0.1757 0.1818 0.19857 0.202 RANDOM 52.338
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] 0.67 -0.8 0.02 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.879 r_dihedral_angle_4_deg 17.128 r_dihedral_angle_3_deg 13.86 r_dihedral_angle_1_deg 5.938 r_long_range_B_refined 5.06 r_long_range_B_other 4.908 r_scangle_other 2.067 r_angle_refined_deg 1.349 r_scbond_it 1.248 r_scbond_other 1.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.879 r_dihedral_angle_4_deg 17.128 r_dihedral_angle_3_deg 13.86 r_dihedral_angle_1_deg 5.938 r_long_range_B_refined 5.06 r_long_range_B_other 4.908 r_scangle_other 2.067 r_angle_refined_deg 1.349 r_scbond_it 1.248 r_scbond_other 1.248 r_mcangle_it 1.165 r_mcangle_other 1.165 r_angle_other_deg 0.914 r_mcbond_it 0.69 r_mcbond_other 0.689 r_chiral_restr 0.08 r_bond_refined_d 0.008 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 11526 Nucleic Acid Atoms Solvent Atoms 875 Heterogen Atoms 318
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing