6NS9

Crystal structure of the IVR-165 (H3N2) influenza virus hemagglutinin apo form


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
3.3162.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.4α = 90
b = 100.4β = 90
c = 382.058γ = 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
11.95501000.150.0412618.15494725
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)
11.952.011000.90.220.922.817.4

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 REPLACEMENTTHROUGHOUT4O5N1.955051993267099.970.167920.166650.19319RANDOM44.227
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]
0.90.450.9-2.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.82
r_dihedral_angle_4_deg18.671
r_dihedral_angle_3_deg14.27
r_long_range_B_refined6.216
r_long_range_B_other6.043
r_dihedral_angle_1_deg5.912
r_scangle_other2.905
r_scbond_it1.64
r_scbond_other1.64
r_angle_refined_deg1.487
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.82
r_dihedral_angle_4_deg18.671
r_dihedral_angle_3_deg14.27
r_long_range_B_refined6.216
r_long_range_B_other6.043
r_dihedral_angle_1_deg5.912
r_scangle_other2.905
r_scbond_it1.64
r_scbond_other1.64
r_angle_refined_deg1.487
r_mcangle_it1.475
r_mcangle_other1.474
r_angle_other_deg0.921
r_mcbond_it0.885
r_mcbond_other0.885
r_chiral_restr0.081
r_bond_refined_d0.01
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 Atoms406
Heterogen Atoms201

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing