9E4R | pdb_00009e4r

Escherichia coli encapsulin-associated DyP peroxidase

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	A0A747AN60

Sample
Escherichia coli KTE40 encapsulin-associated DyP peroxidase

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Grids were frozen with the following parameters: blot force 20, blot time 4 seconds, humidty 100 percent, 22 degrees C.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	10490
Reported Resolution (Å)	3.31
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Local refinement with D3 symmetry and force re-do GS-split applied.
Refinement Type
Symmetry Type	POINT
Point Symmetry	D3

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	cross-correlation coefficient
Overall B Value	105.9
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	47.84	46.24

Imaging Experiment	1	2
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA	TFS GLACIOS
Minimum Defocus (nm)	1000	1000
Maximum Defocus (nm)	1800	1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7	2.7
Imaging Mode	BRIGHT FIELD	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	45000	45000
Calibrated Magnification
Source	FIELD EMISSION GUN	FIELD EMISSION GUN
Acceleration Voltage (kV)	200	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.5.1
IMAGE ACQUISITION	Leginon
CTF CORRECTION	cryoSPARC	4.5.1
MODEL FITTING	UCSF ChimeraX	1.8
IMAGE ACQUISITION	Leginon
MODEL REFINEMENT	PHENIX	1.2.1-4887
MODEL REFINEMENT	Coot	0.9.8.1
INITIAL EULER ASSIGNMENT	cryoSPARC	4.5.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.5.1
RECONSTRUCTION	cryoSPARC	4.5.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		115178