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Near-atomic resolution structure of a plant geminivirus determined by electron cryo-microscopy.
ELECTRON MICROSCOPY
Sample
African cassava mosaic virus - [West Kenya 844]
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Samples (3 ?l) were applied to the glow discharged grids, incubated for 60 s on the grid, blotted and plunge frozen in liquid ethane using a Vitrobot ...
Samples (3 ?l) were applied to the glow discharged grids, incubated for 60 s on the grid, blotted and plunge frozen in liquid ethane using a Vitrobot IV (FEI, Eindhoven, The Netherlands) at 4?C with 100% humidity and blotting from both sides for 3 s with blot force 7
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
24451
Reported Resolution (Å)
4.2
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
D5
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Overall B Value
139
Fitting Procedure
Details
Data Acquisition
Detector Type
FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)
25
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
0.01
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
94000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
RELION
1.4
CTF CORRECTION
RELION
1.4
MODEL FITTING
Coot
MODEL REFINEMENT
PHENIX
INITIAL EULER ASSIGNMENT
RELION
1.4
FINAL EULER ASSIGNMENT
RELION
1.4
CLASSIFICATION
RELION
1.4
RECONSTRUCTION
RELION
1.4
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
141141
For the initial analysis, ca. 2,000 particle images were selected manually with e2boxer and extracted and normalized with relion 1.4 followed by 2D-classification and ctf-correction. Three characteristic class averages that resolved the two parts of the twin particle (side views and intermediate views) were selected as references for template-dependent automatic particle picking in Relion. Particle images were extracted at the determined coordinates with a box size of 300 x 300 Px and normalized for their grey value distribution followed by 2D-classification. Some of the 2D-classes showed disconnected twin particles or single capsids. These classes probably represented either adjacent capsids from different twin particles or incorrectly centered particles and were excluded from the subsequent analysis.
141141 particles is the number of automatically selected particles; 69685 were retained for he subsequent processing