6AOQ

Crystal structure of the A/Brisbane/10/2007 (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 DROP10.52930.1 M CAPS pH 10.5 and 29% PEG 400
Crystal Properties
Matthews coefficientSolvent content
3.3463.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.614α = 90
b = 100.614β = 90
c = 382.62γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9795SSRLBL12-2

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
12.355099.90.110.03134.115.53195343
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)
12.352.431000.840.220.932.815.2

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 REPLACEMENTTHROUGHOUT4O5N2.355030220162699.50.217910.21550.26157RANDOM66.439
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]
1.180.591.18-3.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.855
r_dihedral_angle_4_deg16.254
r_dihedral_angle_3_deg13.769
r_long_range_B_refined7.252
r_long_range_B_other7.108
r_dihedral_angle_1_deg6.12
r_scangle_other3.415
r_scbond_it1.943
r_scbond_other1.943
r_mcangle_it1.892
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.855
r_dihedral_angle_4_deg16.254
r_dihedral_angle_3_deg13.769
r_long_range_B_refined7.252
r_long_range_B_other7.108
r_dihedral_angle_1_deg6.12
r_scangle_other3.415
r_scbond_it1.943
r_scbond_other1.943
r_mcangle_it1.892
r_mcangle_other1.891
r_angle_refined_deg1.462
r_mcbond_it1.121
r_mcbond_other1.121
r_angle_other_deg0.933
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms3867
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms198

Software

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