7T5Q
Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 6.043 |
| f_angle_d | 0.834 |
| f_chiral_restr | 0.049 |
| f_plane_restr | 0.006 |
| f_bond_d | 0.005 |
| Sample |
|---|
| bovine Arp2/3 complex and Actin, CapZ |
| Sample Components |
| bovine Arp2/3 |
| Actin skeletal muscle |
| F-actin-capping protein |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA EM CPC |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Grids were manually blotted for 3 seconds with Whatman 41 filter paper and manually plunged using a Leica EM CPC manual plunger. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 269760 |
| Reported Resolution (Å) | 3.4 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Composite map after multibody refinement |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (4JD2) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | correlation | ||||
| Overall B Value | 132 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1500 |
| Maximum Defocus (nm) | 3500 |
| 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 | 165000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Data were collected in super-resolution mode with an illuminated area of 1.01 um, nominal dose of 40 e-/A^2, a dose rate of 4.87 e-/s/pixel, and 2 or 5 exposures per hole by image shift. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 2.12.4 |
| IMAGE ACQUISITION | Latitude | |
| CTF CORRECTION | CTFFIND | 4.1.13 |
| CTF CORRECTION | cryoSPARC | 2.12.4 |
| MODEL FITTING | Coot | |
| MODEL REFINEMENT | PHENIX | |
| INITIAL EULER ASSIGNMENT | RELION | 3.1 |
| FINAL EULER ASSIGNMENT | RELION | 3.1 |
| CLASSIFICATION | RELION | 3.1 |
| RECONSTRUCTION | cryoSPARC | 4.0 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF correction was done in cryoSPARC for intial 2D classification and then repeated in CTFFIND4 (Relion) for classification and final reconstruction. | 4485066 | Particles autopicked in cryoSPARC | |
