7D6D
Structural insights into membrane remodeling by SNX1
ELECTRON MICROSCOPY
| Sample |
|---|
| sorting nexin 1 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | HELICAL ARRAY |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | blot for 3.5 seconds with a blot force 2 before plunging |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 11795 |
| Reported Resolution (Å) | 9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | IHRSR method were used for helical reconstruction and refinement with a range of out of plane tilt considered |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 8.76 |
| Angular Rotation | 60.13 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | The temperature was kept at 300K, time step was 1 fs, and secondary structure restraints was also included. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON II (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 25 | ||||||||
| 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 | |
| Calibrated Magnification | 59000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | Gctf | 0.50 |
| MODEL FITTING | UCSF Chimera | 1.11.2 |
| MODEL REFINEMENT | NAMD | 2.10 |
| INITIAL EULER ASSIGNMENT | SPIDER | 24.08 |
| FINAL EULER ASSIGNMENT | SPIDER | 24.08 |
| CLASSIFICATION | MATLAB | 2013 |
| RECONSTRUCTION | IHRSR | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF was multiplied to each micrographs before tubes selection, and finally CTF amplitude correction was performed following 3D reconstruction | 476 | All the segments were selected manually using e2helixboxer.py of EMAN2 | |
