Pseudorabies virus (PrV) nuclear egress complex proteins fitted as a hexameric lattice into a sub-tomogram average derived from focused- ion beam milled lamellae electron cryo-microscopic data
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5E8C | |
| Sample |
|---|
| PORCINE EPITHELIAL-LIKE EMBRYONIC EFN-R KIDNEY CELLS STABLY CO- EXPRESSING PRV UL31 AND UL34, THE LATTER FUSED WITH GFP (CELL LINE DESIGNATED AS BK-EF-UL31- 34GFP CATALOGUE NO. RIE 1083 OF THE COLLECTION OF CELL LINES IN VETERINARY MEDICINE AT THE FLI, GREIFSWALD-INSEL RIEMS, GERMANY) |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | CELL |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, INSTRUMENT- HOMEMADE PLUNGER, METHOD- BLOTTED MANUALLY WITH A BENT STRIP OF WHATMAN NO. 1 FILTER P ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | TOMOGRAPHY |
| Number of Particles | 300 |
| Reported Resolution (Å) | 35 |
| Resolution Method | |
| Other Details | FIT OF HEXAMERIC LATTICE OF NEC INTO SUBTOMOGRAM AVERAGE. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3197. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C6 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5E8C) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | MINIMISATION OF ATOMIC CLASHES AND PROTRUSION FROM MAP | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN MULTISCAN | ||||||||
| Electron Dose (electrons/Å**2) | 114 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2013-04-26 |
| Temperature (Kelvin) | |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | -6000 |
| Maximum Defocus (nm) | 6000 |
| Minimum Tilt Angle (degrees) | -50 |
| Maximum Tilt Angle (degrees) | 52 |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 22500 |
| Calibrated Magnification | 52650 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | 2048 X 2048 |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | TEMPy | |
| RECONSTRUCTION | IMOD | |
| RECONSTRUCTION | PEET | |
