ELECTRON MICROSCOPY

Sample

Staphylococcus phage P68

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details blot time 2s; blot force -2; 3.6 ul of sample
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 28826
Reported Resolution (Å) 3.8
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol AB INITIO MODEL
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details The refinement was conducted on rigid body fitted major capsid proteins and Arstotzka proteins obtained from related structure of 6IAT; EMD-4438. The chains were fitted into hexon adjacent to portal of P68 capsid obtained from 5-fold symmetrized reconstruction. Subsequently, poly-alanine chains were manually built into densities corresponding to N-terminal part of head-fiber (chain IDs H,K,L) and C-terminal part of inner core protein (chain IDs X,Y,Z). The map was masked according to the related pdb in chimera, normalized and put into several rounds of a real space refinement in Phenix.
Data Acquisition
Detector Type FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å2) 21
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1.0
Maximum Defocus (nm) 3.0
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.7
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification 75000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION EMAN2 2.1
IMAGE ACQUISITION EPU ?
CTF CORRECTION CTFFIND 4.0
MODEL FITTING Coot 0.8.8
INITIAL EULER ASSIGNMENT RELION 2.1
FINAL EULER ASSIGNMENT RELION 2.1
CLASSIFICATION RELION 2.1
RECONSTRUCTION RELION 2.1
MODEL REFINEMENT PHENIX dev:3042
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?