8TIE
Double nuclear outer ring of Nup84-complexes from the yeast NPC
ELECTRON MICROSCOPY
| Sample |
|---|
| Nuclear Pore Complex |
| Sample Components |
| double Nup84 Y-complex |
| 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 | 29655 |
| Reported Resolution (Å) | 8.1 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | multibody in RELION followed by refinements in cryosparc |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | cross correlation | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Molecular dynamics flexible fitting after docking Alphafold2 CSMs for Nups into the 3D map of double Y complex ring with Chimera | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| 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 | |
| Calibrated Magnification | 37651 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Preliminary grid screening done manually with individual images of low magnification montages of candidate meshes. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Gautomatch | Gautomatch_v0.56_sm61_cu7.5 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | Gctf | Gctf-v0.1.06_sm_20_cu7.5_x86_64 |
| CTF CORRECTION | RELION | 3.0.7 |
| MODEL FITTING | UCSF Chimera | 1.14 |
| MODEL REFINEMENT | MDFF | |
| MODEL REFINEMENT | Coot | 0.8.9.2 |
| INITIAL EULER ASSIGNMENT | RELION | 3.0.7 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 3.3.2 |
| CLASSIFICATION | RELION | 3.0.7 |
| RECONSTRUCTION | cryoSPARC | 3.3.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF correction applied in RELION during the alignment and reconstruction | 26049 | ||
