6D8D

The crystal structure of hemagglutinin from A/Hong Kong/125/2017 influenza virus in complex with LSTb


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LN6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2930.2M Magnesium Acetate, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.2862.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 203.571α = 90
b = 117.866β = 124.21
c = 119.86γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2017-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
13.555099.710.53.726155
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.553.68

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 REPLACEMENTTHROUGHOUT4LN63.5550.0124868129791.890.22310.221160.26033RANDOM69.546
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]
1.3-1.544.94-2.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.163
r_dihedral_angle_3_deg21.227
r_dihedral_angle_4_deg19.304
r_dihedral_angle_1_deg9.181
r_long_range_B_refined7.768
r_long_range_B_other7.768
r_mcangle_it4.6
r_mcangle_other4.6
r_scangle_other3.944
r_mcbond_it2.674
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.163
r_dihedral_angle_3_deg21.227
r_dihedral_angle_4_deg19.304
r_dihedral_angle_1_deg9.181
r_long_range_B_refined7.768
r_long_range_B_other7.768
r_mcangle_it4.6
r_mcangle_other4.6
r_scangle_other3.944
r_mcbond_it2.674
r_mcbond_other2.673
r_scbond_it2.211
r_scbond_other2.211
r_angle_refined_deg2.016
r_angle_other_deg1.155
r_chiral_restr0.101
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms11415
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms255

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing