7MIZ
Atomic structure of cortical microtubule from Toxoplasma gondii
ELECTRON MICROSCOPY
| Sample |
|---|
| cortical microtubule with associated MIPs |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | blot for 4 seconds with a blot force of -15 |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 220139 |
| Reported Resolution (Å) | 3.4 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (4FYU, 6U42, 3JAS) | ||||
| Refinement Space | |||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Secondary structure, Ramachandran, and rotamer restraints were applied during refinement. The nonbonded_weight value was set to 500 to reduce the clas ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 63.7 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | 3500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 0.01 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Appion | 3.2 |
| IMAGE ACQUISITION | EPU | 1.9.0.30REL |
| CTF CORRECTION | Gctf | 1.18 |
| CTF CORRECTION | RELION | 3.1 |
| CTF CORRECTION | cryoSPARC | 2.15 |
| MODEL FITTING | Coot | 0.8 |
| MODEL REFINEMENT | PHENIX | 1.18.2-387464 |
| INITIAL EULER ASSIGNMENT | EMAN | 1.9 |
| FINAL EULER ASSIGNMENT | RELION | 3.1 |
| CLASSIFICATION | RELION | 3.1 |
| RECONSTRUCTION | RELION | 3.1 |
| RECONSTRUCTION | cryoSPARC | 2.15 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF amplitude correction was performed as part of the 3D reconstruction. | 536132 | Cortical MTs were manually picked from the motion-corrected micrographs using the APPION image-processing suite. The selected MT segments were computationally cut into overlapping boxes (512x512 pixels) with an 8-nm non-overlapping region (step size) between adjacent boxes (corresponding to the length of a tubulin heterodimer). We refer to these boxed images as 8-nm MT particles. | |
