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 8A8N | pdb_00008a8n

Structure of self-assembling engineered protein nanocage (EPN) fused with hepatitis A pX protein


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5KP9 
experimental modelPDB 7B3Y 
Sample
EPN-pX
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentGATAN CRYOPLUNGE 3
Cryogen NameETHANE
Sample Vitrification DetailsBlot time 4-5 s.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles1830
Reported Resolution (Å)6.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (5KP9, 7B3Y)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCorrelation coefficient
Overall B Value
Fitting Procedure
DetailsRigid body fit monomer in chimera, generated biological unit then checked in coot and residues to be altered done so in coot followed by one cycle of ...Rigid body fit monomer in chimera, generated biological unit then checked in coot and residues to be altered done so in coot followed by one cycle of rigid body refinement of entire icosahedral assembly in phenix, defining each monomeric unit as a separate body and considering ncs constraints to check for clashes.
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)46
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS GLACIOS
Minimum Defocus (nm)700
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification92000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND
MODEL FITTINGCoot
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTRELION
FINAL EULER ASSIGNMENTRELION
CLASSIFICATIONRELION
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1830Manual selection.