6NHP

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin HA2 I45T mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 38% 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
2.9458.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 209.212α = 90
b = 131.146β = 98.15
c = 72.176γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9795SSRLBL12-2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.255097.40.090.04116.258962138
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)RedundancyNumber Unique Reflections (All)
12.252.3595.70.940.490.681.34.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4FNK2.255084488439097.360.183130.181860.20759RANDOM50.917
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]
1.330.56-0.7-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.598
r_dihedral_angle_4_deg17.134
r_dihedral_angle_3_deg14.503
r_dihedral_angle_1_deg6.101
r_long_range_B_refined5.54
r_long_range_B_other5.492
r_scangle_other3.077
r_mcangle_it1.845
r_mcangle_other1.845
r_scbond_it1.793
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.598
r_dihedral_angle_4_deg17.134
r_dihedral_angle_3_deg14.503
r_dihedral_angle_1_deg6.101
r_long_range_B_refined5.54
r_long_range_B_other5.492
r_scangle_other3.077
r_mcangle_it1.845
r_mcangle_other1.845
r_scbond_it1.793
r_scbond_other1.793
r_angle_refined_deg1.545
r_mcbond_it1.118
r_mcbond_other1.118
r_angle_other_deg0.958
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms11517
Nucleic Acid Atoms
Solvent Atoms666
Heterogen Atoms332

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing