Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex lacking the Mis12c(Mtw1c) head 2 domain
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 5.256 |
| f_angle_d | 0.567 |
| f_chiral_restr | 0.038 |
| f_bond_d | 0.019 |
| f_plane_restr | 0.003 |
| Sample |
|---|
| Saccharomyces cerevisiae outer kinetochore KMN junction complex |
| Sample Components |
| Saccharomyces cerevisiae outer kinetochore Mis12c(Mtw1c) subcomplex |
| Saccharomyces cerevisiae outer kinetochore Knl1c subcomplex |
| Saccharomyces cerevisiae outer kinetochore Ndc80c |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK III |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 113688 |
| Reported Resolution (Å) | 4.9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Composite cryo-EM of two multibody refinement-derived map refined to the consensus map. |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Flexible fitting using Isolde, real-space refinement using Phenix | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1400 |
| Maximum Defocus (nm) | 3000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| 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 | Topaz | |
| MODEL REFINEMENT | PHENIX | 1.21.2_5419: |
| CTF CORRECTION | CTFFIND | 4.1 |
| INITIAL EULER ASSIGNMENT | RELION | 5 |
| FINAL EULER ASSIGNMENT | RELION | 5 |
| CLASSIFICATION | RELION | 5 |
| RECONSTRUCTION | RELION | 5 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 2592458 | Selected using Topaz particle picker trained on manually picked micrographs | ||
