6R22
The structure of a Ty3 retrotransposon capsid N-terminal domain dimer
ELECTRON MICROSCOPY
Sample |
---|
Ty3 capsid N-terminal domain dimer |
Specimen Preparation | |
---|---|
Sample Aggregation State | PARTICLE |
Vitrification Instrument | HOMEMADE PLUNGER |
Cryogen Name | ETHANE |
Sample Vitrification Details | The sample was applied onto glow-discharged C-flat (Protochips Inc.) holey carbon grids. The grids were blotted from the back side for 11 seconds at r ... |
3D Reconstruction | |
---|---|
Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 74160 |
Reported Resolution (Å) | 5.5 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Cross-correlation coefficient | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | FEI FALCON II (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 20 |
Imaging Experiment | 1 |
---|---|
Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 3500 |
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 | Cryo-grids containing purified PR- Ty3 particles were imaged in a Titan Krios electron microscope equipped with a Falcon II direct electron detector, operated at 300 kV. Images were collected with a nominal magnification of 75000, giving a pixel size of 1.08 A. Images were collected in integrating mode with a total electron dose of 20 e/A2. The range of applied defocus values was between -1.0 um and -3.5 um. |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | EMAN2 | |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | CTFFIND | 4 |
MODEL FITTING | MDFF | |
MODEL REFINEMENT | PHENIX | 1.14 |
INITIAL EULER ASSIGNMENT | RELION | |
FINAL EULER ASSIGNMENT | RELION | |
CLASSIFICATION | RELION | |
RECONSTRUCTION | TOM Toolbox |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 1727 |