8OI8
Cryo-EM structure of ADP-bound, filamentous beta-actin harboring the R183W mutation
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 | 11.4735 |
| f_angle_d | 0.5394 |
| f_chiral_restr | 0.0445 |
| f_bond_d | 0.0038 |
| f_plane_restr | 0.0035 |
| Sample |
|---|
| Actin filament harboring the R183W mutation. |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 1386604 |
| Reported Resolution (Å) | 2.28 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Refinement from Local searches in RELION. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | The structure was refined using phenix-real-space refine. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 70 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 800 |
| 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 | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Titan Krios G3 microscope was aligned using Sherpa (FEI). Data collected in superresolution mode. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | crYOLO | 1.5.8 |
| 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 | SPHIRE | 1.4 |
| FINAL EULER ASSIGNMENT | RELION | 3.1.0 |
| CLASSIFICATION | RELION | 3.1.0 |
| RECONSTRUCTION | RELION | 3.1.0 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 1569882 | |||
