7NOE
Structure of the mature RSV CA lattice: Group III, hexamer-hexamer interface, class 3'5
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7NO0 | |
| Sample |
|---|
| Rous sarcoma virus - Prague C |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 2.5 seconds blotting time |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SUBTOMOGRAM AVERAGING |
| Number of Particles | 3546 |
| Reported Resolution (Å) | 7.5 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7NO0) | ||||
| Refinement Space | |||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 3.5 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1500 |
| Maximum Defocus (nm) | 4000 |
| 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 | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Areas of interest for high-resolution data collection were identified in low magnification montages. Prior to tomogram acquisition, gain references were acquired and the filter was fully tuned. Microscope tuning was performed using the FEI AutoCTF software. The ilumination mode used during acquisition was nanoprobe. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| VOLUME SELECTION | MATLAB | R2018b |
| VOLUME SELECTION | IMOD | 4.9 |
| VOLUME SELECTION | Dynamo | 1.1.333 |
| IMAGE ACQUISITION | SerialEM | |
| IMAGE ACQUISITION | DigitalMicrograph | |
| CTF CORRECTION | CTFFIND | 4.1.10 |
| CTF CORRECTION | IMOD | 4.9 |
| CTF CORRECTION | NOVACTF | |
| MODEL FITTING | UCSF Chimera | |
| FINAL EULER ASSIGNMENT | Dynamo | 1.1.333 |
| CLASSIFICATION | MATLAB | R2018b |
| RECONSTRUCTION | Dynamo | 1.1.333 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF-correction was initially performed using ctfphaseflip in IMOD and NovaCTF in the final steps | |||
