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 8C0O | pdb_00008c0o

African cichlid nackednavirus capsid at pH 5.5


ELECTRON MICROSCOPY
Sample
African cichlid nackednavirus
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles77129
Reported Resolution (Å)3.9
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
DetailsOne protein chain was manually built in Coot. The chain was multiplied to give 180 chains, which were arranged as an icosahedral capsid. The capsid wa ...One protein chain was manually built in Coot. The chain was multiplied to give 180 chains, which were arranged as an icosahedral capsid. The capsid was refined with phenix and Isolde.
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)55
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)500
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification166000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcrYOLO1.7.6
IMAGE ACQUISITIONEPU
CTF CORRECTIONGctf1.06
MODEL FITTINGCoot0.8.9
MODEL REFINEMENTPHENIX1.17.1-3660
MODEL REFINEMENTISOLDE1.0b4.dev0
INITIAL EULER ASSIGNMENTRELION3.1
FINAL EULER ASSIGNMENTRELION3.1
CLASSIFICATIONRELION3.1
RECONSTRUCTIONRELION3.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION215225