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 9N8P | pdb_00009n8p

Subtomogram average of dimers of influenza HA trimers


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RVZ 
Sample
Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentEMS-002 RAPID IMMERSION FREEZER
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSUBTOMOGRAM AVERAGING
Number of Particles9283
Reported Resolution (Å)9
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (1RVZ)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsRigid body docking was performed in ChimeraX. Phenix was used for flexible real space refinement and Schrodinger Protein Preparation Wizard was used t ...Rigid body docking was performed in ChimeraX. Phenix was used for flexible real space refinement and Schrodinger Protein Preparation Wizard was used to perform final energy minimization.
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)1.86
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)3000
Maximum Defocus (nm)6000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification42000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
VOLUME SELECTIONWarp
IMAGE ACQUISITIONSerialEM
MODEL FITTINGUCSF ChimeraX
FINAL EULER ASSIGNMENTRELION4
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION