ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7XT8 | |
| in silico model | Other | ColabFold | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 41.16 |
| f_angle_d | 0.608 |
| f_chiral_restr | 0.044 |
| f_plane_restr | 0.005 |
| f_bond_d | 0.003 |
| Sample |
|---|
| UL33-Gas-Gb1-Gg2-Nb35 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 54507 |
| Reported Resolution (Å) | 3.3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | CryoSPARC non-uniform refinement |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7XT8) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | 106.4 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | JEOL CRYO ARM 300 |
| Minimum Defocus (nm) | 600 |
| Maximum Defocus (nm) | 1200 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 3.4 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | |
| Calibrated Magnification | 63291 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | The microscope model is the JEOL's "JEM-Z320FHC", a custom-built model of JEOL CRYO ARM 300. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.6 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | cryoSPARC | 4.6 |
| MODEL FITTING | Coot | 0.9.8.96 EL |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.6 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.6 |
| CLASSIFICATION | cryoSPARC | 4.6 |
| RECONSTRUCTION | cryoSPARC | 4.6 |
| MODEL REFINEMENT | PHENIX | 1.21.1_5286 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CryoSPARC patch CTF estimation and global/local CTF refinements | 1502019 | initial particles that appeared to be protein | |
