Skip to main content

 6I2N | pdb_00006i2n

Helical RNA-bound Hantaan virus nucleocapsid


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FSG 
Sample
RNA-bound Hantaan virus nucleocapsid
Sample Components
Hantaan virus nucleoprotein
RNA
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details3 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 MethodHELICAL
Number of Particles105665
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise18.87
Angular Rotation-99.95
Map-Model Fitting and Refinement
Id1 (5FSG)
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement Target
Overall B Value103
Fitting Procedure
DetailsFiber model was iteratively rebuilt and all-atom refined using stereochemical and NCS restraints
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification46860
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION2.1
IMAGE ACQUISITIONEPU
CTF CORRECTIONGctf
CTF CORRECTIONGctf
CTF CORRECTIONRELION3.0
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTRELION2.1
FINAL EULER ASSIGNMENTRELION2.1
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.13
MODEL REFINEMENTCoot0.8.9
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION168709Straight 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.