ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5OOC | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 9.081 |
| f_angle_d | 0.892 |
| f_chiral_restr | 0.055 |
| f_plane_restr | 0.007 |
| f_bond_d | 0.005 |
| Sample |
|---|
| The actin filament from Zea mays pollen |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blotting time of 5.5 s and blotting force of level 2 |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 35684 |
| Reported Resolution (Å) | 3.9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 27.5 |
| Angular Rotation | -166.77 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5OOC) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | 70 | ||||
| Fitting Procedure | |||||
| Details | Chain C from pdb 5OOC was rigid body fitted to plant actin map using Chimera; Then Phenix was used for real space refinement. Finally, filament with 5 ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 39 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| 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 | 22500 |
| Calibrated Magnification | 22013 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | SPIDER | 24.08 |
| IMAGE ACQUISITION | SerialEM | 3.5 |
| CTF CORRECTION | Gctf | 1.18 |
| MODEL FITTING | UCSF Chimera | 1.10.1 |
| MODEL FITTING | Coot | 7.0 |
| MODEL REFINEMENT | PHENIX | 1.11.1 |
| INITIAL EULER ASSIGNMENT | SPIDER | 24.08 |
| FINAL EULER ASSIGNMENT | SPIDER | 24.08 |
| CLASSIFICATION | SPIDER | 24.08 |
| RECONSTRUCTION | SPIDER | 24.08 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 40943 | A total of 8,609 ZMPA filaments were boxed using e2helixboxer.py in the package of EMAN2 with box width 168 and 77% box-overlap. A total of 40,943 segments were generated with box-size of 384. | ||
