Experiment: 8AAY

Nudaurelia capensis omega virus maturation intermediate captured at pH5.6 (insect cell expressed VLPs): small class from symmetry expansion

ELECTRON MICROSCOPY

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	353898
Reported Resolution (Å)	3.39
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Particles from an I1 icosahedral consensus map (EMD-15266) were symmetry expanded to C1 and further 3D classified without alignment using a soft mask ...	Particles from an I1 icosahedral consensus map (EMD-15266) were symmetry expanded to C1 and further 3D classified without alignment using a soft mask covering the icosahedral asymmetric unit. The particles for this class were randomly split into half sets for the subsequent reconstruction and postprocessing steps. Note that the symmetry expansion step generates a 60-fold larger particle stack.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (7ANM)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	Correlation coefficient
Overall B Value	78
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	49.1

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2500
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	3.0.3
IMAGE ACQUISITION	EPU
CTF CORRECTION	Gctf	1.06
MODEL FITTING	UCSF Chimera	1.14
MODEL FITTING	Coot	0.9
MODEL REFINEMENT	PHENIX	1.20rc4
INITIAL EULER ASSIGNMENT	RELION	3.0.3
FINAL EULER ASSIGNMENT	RELION	3.0.3
CLASSIFICATION	RELION	3.0.3
RECONSTRUCTION	RELION	3.0.3

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