5NZV
The structure of the COPI coat linkage IV
ELECTRON MICROSCOPY
Sample |
---|
The structure of the COPI coat leaf |
Sample Components |
COPI coat complex |
ADP-ribosylation factor 1 |
Specimen Preparation | |
---|---|
Sample Aggregation State | 3D ARRAY |
Vitrification Instrument | HOMEMADE PLUNGER |
Cryogen Name | ETHANE |
Sample Vitrification Details | The sample was applied onto glow-discharged (30 sec, 20 mA) C-flat (Protochips Inc.) multihole grids. The grids were blotted from the back side for 11 ... |
3D Reconstruction | |
---|---|
Reconstruction Method | SUBTOMOGRAM AVERAGING |
Number of Particles | 1640 |
Reported Resolution (Å) | 17.3 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C2 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | Cross-correlation coefficient | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 2 |
Imaging Experiment | 1 |
---|---|
Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 2500 |
Maximum Defocus (nm) | 5000 |
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 | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | Tomographic tilt series were acquired with the dose-symmetric tilt-scheme (Hagen et al., J Struct Biol. 2017) |
EM Software | ||
---|---|---|
Task | Software Package | Version |
VOLUME SELECTION | Amira | |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | CTFFIND | 4 |
MODEL FITTING | UCSF Chimera | 1.11 |
RECONSTRUCTION | TOM Toolbox | |
VOLUME SELECTION | TOM Toolbox | |
CTF CORRECTION | IMOD | |
RECONSTRUCTION | AV3 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING ONLY | CTF-determination for each individual tilt image was performed using CTFFIND4. Strip-based CTF-correction and tomogram reconstruction was performed in Imod. |