8OPE
Virus-like Particle based on PVY coat protein with dC40 deletion with helical architecture encapsidating ssRNA
ELECTRON MICROSCOPY
Sample |
---|
Virus-like particle from dC40 coat protein |
Specimen Preparation | |
---|---|
Sample Aggregation State | FILAMENT |
Vitrification Instrument | |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
---|---|
Reconstruction Method | HELICAL |
Number of Particles | 152296 |
Reported Resolution (Å) | 3.09 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Final cryoEM map was obtained by Phenix density modification. |
Refinement Type | |
Symmetry Type | HELICAL |
Axial Symmetry | C1 |
Axial Rise | 4.05 |
Angular Rotation | -41.05 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | |||||
Refinement Protocol | |||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | FEI FALCON II (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 84 |
Imaging Experiment | 1 |
---|---|
Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | TFS KRIOS |
Minimum Defocus (nm) | 400 |
Maximum Defocus (nm) | 1300 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | 75000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | crYOLO | |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | CTFFIND | 4.1 |
MODEL FITTING | Coot | |
CLASSIFICATION | RELION | |
RECONSTRUCTION | RELION | |
RECONSTRUCTION | PHENIX | |
MODEL REFINEMENT | PHENIX | 1.20 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 2966850 | CrYOLO filament picking based on pre-trained neural network model |