6VFJ

De novo designed icosahedral nanoparticle I53_dn5


ELECTRON MICROSCOPY
Sample
De novo designed nanoparticle of icosahedral symmetry I53_dn5_NP
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details0.06mM DDM detergent (from an 8X stock) added immediately before freezing
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles31353
Reported Resolution (Å)5.35
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value
Fitting Procedure
DetailsIcosahedral nanoparticle I53_dn5 model was docked into a reconstructed map using UCSF Chimera and Rosetta relaxed refinement was applied to relax the ...Icosahedral nanoparticle I53_dn5 model was docked into a reconstructed map using UCSF Chimera and Rosetta relaxed refinement was applied to relax the model into the map.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)50.4
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)600
Maximum Defocus (nm)1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification29000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC2.9.0
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 ONLY207651