9QVE | pdb_00009qve

Satellite Tobacco Necrosis Virus-1

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZX8

Sample
Satellite tobacco necrosis virus 1

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	207142
Reported Resolution (Å)	2.77
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (2BUK)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	cross-correlation coefficient
Overall B Value	43
Fitting Procedure
Details

Data Acquisition
Detector Type	TFS FALCON 4i (4k x 4k)	TFS FALCON 4i (4k x 4k)	TFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)	30	30	40

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS TALOS F200C
Minimum Defocus (nm)	700
Maximum Defocus (nm)	1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Nominal Magnification	150000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.5.3
IMAGE ACQUISITION	EPU	3.7.1.6940
CTF CORRECTION	cryoSPARC	4.5.3
MODEL FITTING	UCSF ChimeraX	1.8
MODEL FITTING	Coot	0.9.8.95 EL (ccp4)
INITIAL EULER ASSIGNMENT	cryoSPARC	4.5.3
FINAL EULER ASSIGNMENT	cryoSPARC	4.5.3
CLASSIFICATION	cryoSPARC	4.5.3
RECONSTRUCTION	cryoSPARC	4.5.3
MODEL REFINEMENT	PHENIX	1.21.2_5419:

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		2394377	combined figure from the 3 datasets