7BJP
The cryo-EM structure of vesivirus 2117, an adventitious agent and possible cause of haemorrhagic gastroenteritis in dogs.
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 9.247 |
| f_angle_d | 0.986 |
| f_chiral_restr | 0.063 |
| f_bond_d | 0.012 |
| f_plane_restr | 0.007 |
| Sample |
|---|
| Calicivirus isolate 2117 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Sample was loaded onto C-flat C1.2/1.3 grids bearing a thin continuous carbon film, allowed to adsorb for one minute before blotting for 3 seconds and ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 15989 |
| Reported Resolution (Å) | 3.65 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | |||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | DIRECT ELECTRON DE-64 (8k x 8k) | ||||||||
| Electron Dose (electrons/Å**2) | 55 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | JEOL CRYO ARM 300 |
| 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 | JEOL CRYOSPECPORTER |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | JADAS | |
| CTF CORRECTION | Gctf | |
| CTF CORRECTION | RELION | 3.0.3 |
| MODEL FITTING | Coot | |
| INITIAL EULER ASSIGNMENT | RELION | 3.0.3 |
| FINAL EULER ASSIGNMENT | RELION | 3.0.3 |
| CLASSIFICATION | RELION | 3.0.3 |
| RECONSTRUCTION | RELION | 3.0.3 |
| MODEL REFINEMENT | PHENIX | |
| MODEL REFINEMENT | REFMAC | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 65071 | Automated particle picking was performed using RELION | ||
