6BKR

Crystal structure of the A/Wyoming/3/2003 (H3N2) influenza virus hemagglutinin in complex with 6'-SLN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4O5N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92930.1 M bicine pH 9 and 42% 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
3.3563.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.458α = 90
b = 100.458β = 90
c = 385.692γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B

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
11.765099.30.090.02152187440821
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)
11.761.8292.50.480.130.953.614.5

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 REPLACEMENTTHROUGHOUT4O5N1.765070663374399.850.160350.159110.18332RANDOM33.597
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]
0.50.250.5-1.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.719
r_dihedral_angle_4_deg18.867
r_dihedral_angle_3_deg13.593
r_long_range_B_refined6.743
r_dihedral_angle_1_deg6.099
r_long_range_B_other6.002
r_scangle_other2.494
r_angle_refined_deg1.53
r_scbond_it1.513
r_scbond_other1.512
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.719
r_dihedral_angle_4_deg18.867
r_dihedral_angle_3_deg13.593
r_long_range_B_refined6.743
r_dihedral_angle_1_deg6.099
r_long_range_B_other6.002
r_scangle_other2.494
r_angle_refined_deg1.53
r_scbond_it1.513
r_scbond_other1.512
r_mcangle_it1.403
r_mcangle_other1.402
r_angle_other_deg0.957
r_mcbond_it0.845
r_mcbond_other0.845
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms3869
Nucleic Acid Atoms
Solvent Atoms543
Heterogen Atoms255

Software

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