6NSB

Crystal structure of the IVR-165 (H3N2) influenza virus hemagglutinin in complex with 6'-SLNLN


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27744% 2-methyl-2,4-pentanediol, 0.1 M HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.463.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.123α = 90
b = 101.123β = 90
c = 387.229γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-04-23MSINGLE 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
11.75501000.130.0213937.77688825
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)
11.751.811001.330.230.921.8

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 REPLACEMENTTHROUGHOUT4O5N1.755073049382599.830.165940.164840.18686RANDOM38.025
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]
0.60.30.6-1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.445
r_dihedral_angle_4_deg17.404
r_dihedral_angle_3_deg13.867
r_long_range_B_refined6.56
r_long_range_B_other6.143
r_dihedral_angle_1_deg5.897
r_scangle_other2.973
r_scbond_it1.719
r_scbond_other1.719
r_angle_refined_deg1.529
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.445
r_dihedral_angle_4_deg17.404
r_dihedral_angle_3_deg13.867
r_long_range_B_refined6.56
r_long_range_B_other6.143
r_dihedral_angle_1_deg5.897
r_scangle_other2.973
r_scbond_it1.719
r_scbond_other1.719
r_angle_refined_deg1.529
r_mcangle_it1.412
r_mcangle_other1.411
r_angle_other_deg0.949
r_mcbond_it0.872
r_mcbond_other0.872
r_chiral_restr0.087
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 Atoms3879
Nucleic Acid Atoms
Solvent Atoms518
Heterogen Atoms261

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing