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 6VFK | pdb_00006vfk

De novo designed tetrahedral nanoparticle T33_dn10 displaying 4 copies of BG505-SOSIP trimer on the surface


ELECTRON MICROSCOPY
Sample
De novo designed tetrahedral nanoparticle T33_dn10 displaying 4 copies of BG505-SOSIP trimer on the surface. Nanoparticle consists of 12 copies of both subunits (BG505-SOSIP-T33_dn10A and T33_dn10B)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlotting time varied in the 3-7 s range, Blotting force set to 0, Wait time of 10s.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles81105
Reported Resolution (Å)4.25
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryT
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsModel refinement was performed by iterative rounds of Rosetta relaxed refinement and manual refinement in Coot.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)49.39
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TALOS ARCTICA
Minimum Defocus (nm)600
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelOTHER
Nominal Magnification36000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC
IMAGE ACQUISITIONLeginon
CTF CORRECTIONRELION3.0
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTRELION3.0
FINAL EULER ASSIGNMENTRELION3.0
CLASSIFICATIONRELION3.0
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTRosetta
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLY25791Template picking in cryoSPARC