6I2N
Helical RNA-bound Hantaan virus nucleocapsid
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5FSG |
Sample |
---|
RNA-bound Hantaan virus nucleocapsid |
Sample Components |
Hantaan virus nucleoprotein |
RNA |
Specimen Preparation | |
---|---|
Sample Aggregation State | FILAMENT |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 3 ul of sample were applied on the resulting glow-discharged grids and excess solution was blotted during 2.5 sec force 7 |
3D Reconstruction | |
---|---|
Reconstruction Method | HELICAL |
Number of Particles | 105665 |
Reported Resolution (Å) | 3.3 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | HELICAL |
Axial Symmetry | C1 |
Axial Rise | 18.87 |
Angular Rotation | -99.95 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (5FSG) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | AB INITIO MODEL | ||||
Refinement Target | |||||
Overall B Value | 103 | ||||
Fitting Procedure | |||||
Details | Fiber model was iteratively rebuilt and all-atom refined using stereochemical and NCS restraints |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40 |
Imaging Experiment | 1 |
---|---|
Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
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 | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | |
Calibrated Magnification | 46860 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | RELION | 2.1 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | Gctf | |
CTF CORRECTION | Gctf | |
CTF CORRECTION | RELION | 3.0 |
MODEL FITTING | UCSF Chimera | |
INITIAL EULER ASSIGNMENT | RELION | 2.1 |
FINAL EULER ASSIGNMENT | RELION | 2.1 |
RECONSTRUCTION | RELION | 3.0 |
MODEL REFINEMENT | PHENIX | 1.13 |
MODEL REFINEMENT | Coot | 0.8.9 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 168709 | Straight HTNV-NC were manually picked and computationally cut with an inter-box distance of 38 A along the helical axis into overlapping boxes of 400*400 pixels, resulting in 168,709 extracted segments. 2D classification was used to eliminate bad quality filaments. |