6NSA

Crystal structure of the IVR-165 (H3N2) influenza virus hemagglutinin in complex with 3'-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
3.4364.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.462α = 90
b = 101.462β = 90
c = 388.077γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.9765ALS5.0.3

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
11.955099.70.110.04133.57.55665728
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)
11.952.0299.40.990.380.867.5

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 REPLACEMENTTHROUGHOUT4O5N1.955053635284099.620.180840.179420.20757RANDOM42.319
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]
1.10.551.1-3.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.954
r_dihedral_angle_4_deg17.264
r_dihedral_angle_3_deg14.133
r_long_range_B_refined6.259
r_dihedral_angle_1_deg6.2
r_long_range_B_other6.034
r_scangle_other3.025
r_scbond_it1.719
r_scbond_other1.716
r_angle_refined_deg1.515
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.954
r_dihedral_angle_4_deg17.264
r_dihedral_angle_3_deg14.133
r_long_range_B_refined6.259
r_dihedral_angle_1_deg6.2
r_long_range_B_other6.034
r_scangle_other3.025
r_scbond_it1.719
r_scbond_other1.716
r_angle_refined_deg1.515
r_mcangle_it1.502
r_mcangle_other1.501
r_angle_other_deg0.955
r_mcbond_other0.898
r_mcbond_it0.897
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms3852
Nucleic Acid Atoms
Solvent Atoms423
Heterogen Atoms316

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing