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 8AYX | pdb_00008ayx

Poliovirus type 3 (strain Saukett) stabilised virus-like particle (PV3 SC8) in complex with GSH and GPP3


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PVC 
Sample
Human poliovirus 3
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE-PROPANE
Sample Vitrification Details4 ul of sample blotted for 3.5 seconds with -15 blot force on FEI Vitrobot mark IV.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles5364
Reported Resolution (Å)2.5
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsFinal reconstruction was sharpened with Post-processing in RELION using an inverse B-factor of -52.3 Angstroms.
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (1PVC)
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 TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)34.89
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2900
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeDARK FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification75000
Calibrated Magnification129629
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcrYOLO1.5.6
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 CORRECTION19622Automated particle picking using crYOLO.