6EHL | pdb_00006ehl

Model of the Ebola virus nucleoprotein in recombinant nucleocapsid-like assemblies

ELECTRON MICROSCOPY

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Sample
Ebola virus - Mayinga, Zaire, 1976

Specimen Preparation
Sample Aggregation State	HELICAL ARRAY
Vitrification Instrument	FEI VITROBOT MARK II
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SUBTOMOGRAM AVERAGING
Number of Particles	1
Reported Resolution (Å)	6.6
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Local resolution was estimated using moving window FSC calculations.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Crystal structure was rigid-body fitted into density using Chimera. Missing regions of the structure was built using ideal secondary structures in coot. These were then flexibly fit using MDFF and NAMD.

Data Acquisition
Detector Type	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	2.4

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	2000
Maximum Defocus (nm)	4500
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	81000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
VOLUME SELECTION	Amira	4
VOLUME SELECTION	TOM Toolbox
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	CTFFIND	4
CTF CORRECTION	CTFPHASEFLIP
MODEL FITTING	UCSF Chimera
MODEL REFINEMENT	Coot
MODEL REFINEMENT	NAMD
FINAL EULER ASSIGNMENT	AV3
RECONSTRUCTION	AV3
MODEL REFINEMENT	MDFF

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING ONLY	CTF amplitude correction was performed during the wedge-weighted subtomogram averaging step.