9TIR | pdb_00009tir

Phage 812 baseplate in the post-contraction state (C6)


ELECTRON MICROSCOPY
Sample
Staphylococcus phage 812K1/420
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles21264
Reported Resolution (Å)4.4
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC6
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsFitting of previously refined sub-models (e.g. arm, core and wedge modules, baseplate-proximal tail) in ChimeraX as rigid bodies, then relaxing the mo ...Fitting of previously refined sub-models (e.g. arm, core and wedge modules, baseplate-proximal tail) in ChimeraX as rigid bodies, then relaxing the model using ISOLDE before rigid body refinement in Phenix (all chains as a single rigid body).
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)42
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONTopaz
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONGctf
MODEL FITTINGUCSF ChimeraX
INITIAL EULER ASSIGNMENTRELION4.0
FINAL EULER ASSIGNMENTRELION4.0
RECONSTRUCTIONRELION5.0
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION54841