6H2B
Structure of the Macrobrachium rosenbergii Nodavirus
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 8.816 |
| f_angle_d | 0.843 |
| f_chiral_restr | 0.059 |
| f_bond_d | 0.007 |
| f_plane_restr | 0.004 |
| Sample |
|---|
| Macrobrachium rosenbergii nodavirus |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | VLPs were deposited onto a continuous carbon film that had been floated onto a quantifoil holey carbon film (R2/2) |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 40883 |
| Reported Resolution (Å) | 3.28 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Standard Relion workflow for icosahedral particle. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | |||||
| Overall B Value | 140 | ||||
| Fitting Procedure | |||||
| Details | Model built largely ab initio, following docking of a homology model based on PDB 4LLF. The homology model matched in two strands at residues - 104-13 ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 36 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 2500 |
| 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 | 47170 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | RELION | 2.1 |
| MODEL FITTING | Coot | |
| INITIAL EULER ASSIGNMENT | RELION | 2.1 |
| FINAL EULER ASSIGNMENT | RELION | 2.1 |
| CLASSIFICATION | RELION | |
| RECONSTRUCTION | RELION | 2.1 |
| MODEL REFINEMENT | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 60939 | Automated particle picking in Relion 2.1 | ||
