8VBX

ELECTRON MICROSCOPY

Sample

Pectobacterium phage PhiM1

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 17132
Reported Resolution (Å) 3.23
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 FLEXIBLE FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details Initial models were developed using AlphaFold-2, and were docked into EM maps. Models were then flexibly fit using chimeraX, followed by manual refinement using a combination of ISOLDE (ChimeraX) and coot. Automatic refinements were performed in PHENIX real space refine.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 53.9
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS KRIOS
Minimum Defocus (nm) 800
Maximum Defocus (nm) 2400
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.7
Imaging Mode BRIGHT FIELD
Specimen Holder Model ?
Nominal Magnification 64000
Calibrated Magnification 36765
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 4.2.1
IMAGE ACQUISITION EPU ?
CTF CORRECTION cryoSPARC 4.2.1
MODEL FITTING UCSF ChimeraX 1.6
MODEL REFINEMENT ISOLDE 1.6
MODEL REFINEMENT Coot 0.9.5
INITIAL EULER ASSIGNMENT cryoSPARC 4.2.1
FINAL EULER ASSIGNMENT cryoSPARC 4.2.1
CLASSIFICATION cryoSPARC 4.2.1
RECONSTRUCTION cryoSPARC 3.2.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION Patch based CTF correction.