8OI6
Cryo-EM structure of the undecorated barbed end of filamentous beta/gamma actin
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8A2T | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 5.3048 |
| f_angle_d | 0.5606 |
| f_chiral_restr | 0.0417 |
| f_plane_restr | 0.0033 |
| f_bond_d | 0.0021 |
| Sample |
|---|
| actin-phalloidin complex |
| Sample Components |
| cytosolic beta-gamma actin |
| phalloidin |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 43618 |
| Reported Resolution (Å) | 3.59 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Performed in CryoSPARC. All barbed end particles were isolated from from other particles that represented pointed end and filament core. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (8A2T) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Real space refinement in phenix. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 56 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TALOS ARCTICA |
| Minimum Defocus (nm) | 1200 |
| 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 | 120000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details | Microsope alignment was performed using SHERPA (Thermo Fisher) |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | crYOLO | 1.8 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | CTFFIND | 4.13 |
| MODEL FITTING | Coot | 0.9.8.1 |
| MODEL REFINEMENT | PHENIX | 1.20.1-4487-000 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 3.3.2 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 3.3.2 |
| CLASSIFICATION | cryoSPARC | 3.3.2 |
| RECONSTRUCTION | cryoSPARC | 3.3.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 252982 | CrYOLO was trained to pick filament ends. | ||
