5UK0

CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 2


ELECTRON MICROSCOPY
Sample
Influenza-virus hemagglutinin H1 complexed with K1915 single-chain variable-domain fragment
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK I
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles142314
Reported Resolution (Å)4.8
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsRefinement and classification were limited to 10 Angstrom resolution.
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement TargetCorrelation coefficient
Overall B Value
Fitting Procedure
DetailsDomains were initially placed manually using Chimera. The HA trimer was from PDB ID 5UGY. Fab was initially obtained using MODELLER, with PDB ID 4K8R ...Domains were initially placed manually using Chimera. The HA trimer was from PDB ID 5UGY. Fab was initially obtained using MODELLER, with PDB ID 4K8R as template. The structure was refined using PHENIX.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification18000
Calibrated Magnification30444
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONCTFFIND3
MODEL FITTINGManual placement
INITIAL EULER ASSIGNMENTIMAGIC
FINAL EULER ASSIGNMENTFREALIGN9.11
CLASSIFICATIONFREALIGN9.11
RECONSTRUCTIONFREALIGN9.11
MODEL REFINEMENTPHENIX1.10_2155
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION252130