6WXF
Cryo-EM reconstruction of VP5*/VP8* assembly from rhesus rotavirus particles - Intermediate conformation
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 11.5409 |
| f_angle_d | 0.6828 |
| f_chiral_restr | 0.0443 |
| f_plane_restr | 0.0044 |
| f_bond_d | 0.0037 |
| Sample |
|---|
| Rotavirus VP4, VP6, VP7 assembly in an intermediate confromattion |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | GATAN CRYOPLUNGE 3 |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 4 ul sample volume, 4 sec blotting time |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 82008 |
| Reported Resolution (Å) | 4.3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Reconstruction final map after classification of VP4 sub-particles . VP4 sub-particles extracted from viral particles (60 VP4 sub-particles per viral ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (4V7Q, 1SLQ) | ||||
| Refinement Space | |||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | phenix.real_space_refine | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 33 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 3000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 27500 |
| Calibrated Magnification | 40605 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | Gctf | |
| MODEL FITTING | O | |
| MODEL REFINEMENT | PHENIX | 1.17.1-3660 |
| INITIAL EULER ASSIGNMENT | cisTEM | |
| FINAL EULER ASSIGNMENT | cisTEM | |
| CLASSIFICATION | cisTEM | |
| RECONSTRUCTION | cisTEM | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 3522 | whole viral particles | ||
