6V8I

Composite atomic model of the Staphylococcus aureus phage 80alpha baseplate


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5EFV 
Sample
Staphylococcus phage 80alpha baseplate
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles43601
Reported Resolution (Å)3.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC6
Map-Model Fitting and Refinement
Id1 (5EFV)
Refinement SpaceRECIPROCAL
Refinement ProtocolRIGID BODY FIT
Refinement Targetcorrelation coefficient
Overall B Value
Fitting Procedure
DetailsInitial models derived from I-TASSER predictions based on GenBank sequences of modeled proteins. Rigid body fitting in UCSF Chimera followed by manual ...Initial models derived from I-TASSER predictions based on GenBank sequences of modeled proteins. Rigid body fitting in UCSF Chimera followed by manual extension in Coot.
Data Acquisition
Detector TypeDIRECT ELECTRON DE-20 (5k x 3k)
Electron Dose (electrons/Å**2)104.33
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1700
Maximum Defocus (nm)3700
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Nominal Magnification29000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION2.0
IMAGE ACQUISITIONLeginon
IMAGE ACQUISITIONAppion
CTF CORRECTIONGctf1.06_sm_30_cu8.0_x86_64
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTRELION2.0
FINAL EULER ASSIGNMENTRELION3.0-beta-2
CLASSIFICATIONRELION3.0-beta-2
RECONSTRUCTIONRELION3.0-beta-2
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLY515106