7KPN
Adeno-associated virus serotype 5 in complex with the cellular receptor AAVR at 2.5 Angstroms resolution, AAV5 AAVR
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3NTT | |
| Sample |
|---|
| Adeno-associated virus - 5 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Two 2uL aliquots applied to grid (manual blotting between), prior to automated 3 second blot before plunging. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 159673 |
| Reported Resolution (Å) | 2.5 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3NTT) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Least-squares residual | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Stand-alone RSRef was used for refinement of magnification, resolution, envelope correction and atomic B-factors. This was alternated with RSRef-embed ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 32.9 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | -700 |
| Maximum Defocus (nm) | -2700 |
| 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 | 64000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 3.0 |
| CTF CORRECTION | CTFFIND | 4 |
| MODEL FITTING | Coot | 0.8.9.2 |
| MODEL REFINEMENT | RSRef | 0.5.8 |
| MODEL REFINEMENT | CNS | 1.3 |
| INITIAL EULER ASSIGNMENT | RELION | 3.0 |
| FINAL EULER ASSIGNMENT | RELION | 3.0 |
| CLASSIFICATION | RELION | 3.0 |
| RECONSTRUCTION | RELION | 3.0 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | CTF correction was performed on a per particle basis. | 168275 | LoG Picker was used for initial automated particle selection. Templates were then generated by 2D classification, followed by particle template selection in Relion 3.0. | |
