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 8AYZ | pdb_00008ayz

Poliovirus type 2 (strain MEF-1) virus-like particle in complex with capsid binder compound 17


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EAH 
Sample
Human poliovirus 2
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE-PROPANE
Sample Vitrification DetailsSingle blotting with 3.5ul of sample. Four second blot time and -17 blot force on the vitrobot.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles51518
Reported Resolution (Å)1.88
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsFinal reconstruction was Ewald sphere corrected and sharpened with Post-processing in RELION using an inverse B-factor of -15.0 Angstroms. B-factor w ...Final reconstruction was Ewald sphere corrected and sharpened with Post-processing in RELION using an inverse B-factor of -15.0 Angstroms. B-factor was selected ad-hoc while testing a range of values for map interpretability.
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (1EAH)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCorrelation coefficient
Overall B Value
Fitting Procedure
DetailsInitial model was rigid body fitted using UCSF chimera and Coot. Global minimization and B-factor refinement was performed in real space using pheni ...Initial model was rigid body fitted using UCSF chimera and Coot. Global minimization and B-factor refinement was performed in real space using phenix_real.space.refine.
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)34.68
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2300
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification60314
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONETHAN
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4.0
MODEL FITTINGUCSF Chimera1.14
INITIAL EULER ASSIGNMENTRELION3.1.1
FINAL EULER ASSIGNMENTRELION3.1.1
CLASSIFICATIONRELION3.1.1
RECONSTRUCTIONRELION3.1.1
MODEL REFINEMENTPHENIX1.19.2-4158-000
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION157002Particle selection was automated with ETHAN particle picking software.