Sub-2 Angstrom Ewald Curvature-Corrected Single-Particle Cryo-EM Reconstruction of AAV-2 L336C
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1LP3 | |
| Sample |
|---|
| Adeno-associated virus - 2 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Double blotting was used to increase particle concentration. Sample was added to a plasma-cleaned (Gatan Solarus) grid and blotted away using Whatman ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 30515 |
| Reported Resolution (Å) | 1.86 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Frequency limited refinement |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1LP3) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Correlation coefficient, EM ringer score | ||||
| Overall B Value | 61.9 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 22.5 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 600 |
| Maximum Defocus (nm) | 2000 |
| 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 | 37000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Beam tilt in 8 directions +/- 5 mrad |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Gautomatch | 0.56 |
| IMAGE ACQUISITION | Leginon | |
| CTF CORRECTION | RELION | 2.1 |
| MODEL FITTING | Coot | 0.8.9.1 |
| MODEL REFINEMENT | PHENIX | 1.13 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 0.65 |
| FINAL EULER ASSIGNMENT | FREALIGN | 9.11 |
| CLASSIFICATION | FREALIGN | 9.11 |
| RECONSTRUCTION | FREALIGN | 9.11 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF estimation per particle - Gctf, CTF estimation per micrograph - CTFFIND4 | 78194 | Template-based picking by generating template from a 2-D classification of an initial subset of data. | |
