Pseudoatomic model of the pre-fusion conformation of glycoprotein B of Herpes simplex virus 1
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5V2S | |
| Sample |
|---|
| Human alphaherpesvirus 1 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SUBTOMOGRAM AVERAGING |
| Number of Particles | 46067 |
| Reported Resolution (Å) | 9.1 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C3 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5V2S) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Cross correlation coefficient | ||||
| Overall B Value | 300 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 2.3 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | OTHER |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Additional Dataset collected using Titan Krios (FEI Thermo) at 300 kV with a 70 um C2 aperture and post-column QUANTUM energy filter operated in Zero-Loss mode using 20 eV energy slit and K2 Summit direct electron detector in counting mode (Gatan). Defocus range: 2300 - 4900 nm. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| VOLUME SELECTION | 3dmod | |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | NOVACTF | |
| CTF CORRECTION | CTFPHASEFLIP | |
| MODEL FITTING | UCSF Chimera | |
| FINAL EULER ASSIGNMENT | PEET | |
| RECONSTRUCTION | PEET | |
| MODEL REFINEMENT | MDFF | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | ||||
