8TK7

Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7S2T

Sample
Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein
Sample Components
Myxococcus xanthus EncA encapsulin shell protein
SNAP-Tag/EncC targeting peptide

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	50680
Reported Resolution (Å)	2.53
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (7S2T)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation coefficient
Overall B Value	89.9
Fitting Procedure
Details	The model was initially fit into the map using UCSF ChimeraX. It was then manually refined using Coot, followed by real-space refinement against the m ...	The model was initially fit into the map using UCSF ChimeraX. It was then manually refined using Coot, followed by real-space refinement against the map using Phenix.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	49.26

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2500
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	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.2.1
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC	4.2.1
MODEL FITTING	UCSF ChimeraX	1.15
INITIAL EULER ASSIGNMENT	cryoSPARC	4.2.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.2.1
RECONSTRUCTION	cryoSPARC	4.2.1
MODEL REFINEMENT	Coot	0.9.8.1
MODEL REFINEMENT	PHENIX	1.20.1-4487

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.