Cryo-EM structure of a 2:1 ALK:ALKAL2 complex obtained after re-processing of EMPIAR-10930 data
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7N00 | |
| Sample |
|---|
| Cryo-EM structure of a 2:1 ALK:ALKAL2 complex obtained after re-processing of EMPIAR-10930 data |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | QUANTIFOIL R1.2/1/3 gold 300 mesh grids without glow-discharge, blotting time 3 sec., blotting force -5. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 142986 |
| Reported Resolution (Å) | 3.2 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Final 3D refinement was performed in Relion v5 with enabled Blush Regularization. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7N00) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Rigid-body fitting in Chimera was followed by manual building in Coot and refinement using Phenix real-space refine and Refmac-Servalcat. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 81 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 500 |
| Maximum Defocus (nm) | 1500 |
| 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 | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | SerialEM coma-free alignment |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 3.3.1 |
| CTF CORRECTION | cryoSPARC | 3.3.1 |
| MODEL FITTING | UCSF Chimera | |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.5 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.5 |
| CLASSIFICATION | cryoSPARC | 4.5 |
| RECONSTRUCTION | RELION | 5 |
| MODEL REFINEMENT | PHENIX | 1.19.2-4158 |
| MODEL REFINEMENT | REFMAC | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 18053705 | |||
