8R69 | pdb_00008r69

Neck and tail of phage 812 virion (composite)

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8QJE
experimental model	PDB	8QKH
experimental model	PDB	8R5G

Sample
Staphylococcus phage 812

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	21731
Reported Resolution (Å)	4.3
Resolution Method	OTHER
Other Details	This is a composite map created by merging two focused reconstructions. The composite map was then low-pass filtered to the (gold-standard cut-off 0.143) resolution of the input reconstruction with worse resolution.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C6

Map-Model Fitting and Refinement
Id	1 (8QJE, 8QKH, 8R5G)
Refinement Space
Refinement Protocol	RIGID BODY FIT
Refinement Target	cross-correlation coefficient
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)	49

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1200
Maximum Defocus (nm)	2400
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	75000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	EMAN2
IMAGE ACQUISITION	EPU
CTF CORRECTION	Gctf	1.0.6
MODEL FITTING	UCSF Chimera	1.16
INITIAL EULER ASSIGNMENT	RELION	3.1
FINAL EULER ASSIGNMENT	RELION	3.1
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	RELION	3.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		23947	Manual particle selection