7ATA | pdb_00007ata

Nudaurelia capensis omega virus procapsid: virus-like particles expressed in Nicotiana benthamiana

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ANM

Sample
Nudaurelia capensis omega virus

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	5426
Reported Resolution (Å)	6.63
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (7ANM)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	Correlation coefficient
Overall B Value	105.8
Fitting Procedure
Details	The model was built and refined against a density modified map generated using phenix.resolve_cryo_em. This used the Relion half maps as inputs and improved the resolution to 6.6 Angstrom.

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	72

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	700
Maximum Defocus (nm)	2700
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	75000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	3.1
IMAGE ACQUISITION	EPU
CTF CORRECTION	Gctf	1.06
MODEL FITTING	UCSF Chimera	1.14
MODEL FITTING	Coot	0.9
INITIAL EULER ASSIGNMENT	RELION	3.1
FINAL EULER ASSIGNMENT	RELION	3.1
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.18.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	NULL