8R3Y
Cryo EM structure of a stable LGL/aPKC Iota/Par-6 complex
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | THIS STUDY | |
| experimental model | PDB | 1NF3 | |
| experimental model | PDB | 6N8Q | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 13.279 |
| f_angle_d | 3.576 |
| f_chiral_restr | 0.158 |
| f_bond_d | 0.039 |
| f_plane_restr | 0.03 |
| Sample |
|---|
| aPKCiota-Par6-Llgl1 complex |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 4 ul of aPKCiota-Par6-Llgl1 complex at a concentration of 0.4 mg/ml was applied to R1.2/1.3 Quantifoil 300 mesh copper grids which had been glow-disch ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 121194 |
| Reported Resolution (?) | 3.68 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (8R3X, 1NF3, 6N8Q) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Initial fitting was done in Chimera. Interactive Model building was done in COOT & Isolde Refinement was done using Phenix. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/?**2) | 48.1 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1200 |
| 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 | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Xmipp | 3 |
| PARTICLE SELECTION | Gautomatch | |
| PARTICLE SELECTION | RELION | 3 |
| CTF CORRECTION | CTFFIND | 2 |
| MODEL FITTING | UCSF Chimera | |
| MODEL FITTING | Coot | 0.9.8 |
| MODEL FITTING | ISOLDE | |
| RECONSTRUCTION | cryoSPARC | 2 |
| MODEL REFINEMENT | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | 1069057 | Semi-automated picking with Xmipp3 and particle extraction in Relion-3 yielded 47,516 particles from 1000 micrographs 38. After reference-free 2D classification in Relion-3, eight 2D classes were selected and used as templates for reference-based particle picking in Gautomatch. A total of particles were extracted with 2-fold binning and submitted to 8 rounds of 2D classification in Relion-3. | ||
