6OUC | pdb_00006ouc

Asymmetric focsued reconstruction of human norovirus GII.2 Snow Mountain Virus strain VLP asymmetric unit in T=1 symmetry

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RPB

Sample
Snow Mountain virus

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	1486080
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Symmetry expansion and signal subtraction of the icosahedral asymmetric units from the whole particle images, followed by asymmetric focused reconstruction towards the apex of the spike domain
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (4RPB)
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	69

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1200
Maximum Defocus (nm)	2600
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	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cisTEM	1.0.0
IMAGE ACQUISITION	EPU	1.10
CTF CORRECTION	cisTEM	1.0.0
MODEL FITTING	MOLREP	CCPEM
MODEL FITTING	Coot	0.8.9
MODEL REFINEMENT	PHENIX	1.14
INITIAL EULER ASSIGNMENT	cisTEM	1.0.0
FINAL EULER ASSIGNMENT	cisTEM	1.0.0
CLASSIFICATION	cisTEM	1.0.0
RECONSTRUCTION	cisTEM	1.0.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING ONLY		76405