9BJE | pdb_00009bje

Encapsulin 1 of a two-component Family 2B encapsulin shell from Streptomyces lydicus

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9BIX

Sample
A two-component Family 2B encapsulin shell from Streptomyces lydicus with Encapsulin 1 enriched
Sample Components
Encapsulin 2 of a two-component Family 2B encapsulin shell from Streptomyces lydicus

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blot force: 20 Blot time: 4 seconds Wait time: 0 seconds

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	69590
Reported Resolution (Å)	2.58
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Homogeneous refinement was performed against the ab-initio map with I symmetry, per-particle defocus optimization, per-group CTF parameterization, and ...	Homogeneous refinement was performed against the ab-initio map with I symmetry, per-particle defocus optimization, per-group CTF parameterization, and Ewald sphere correction with negative curvature.
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (9BIX)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	correlation coefficient
Overall B Value	99.9
Fitting Procedure
Details	The starting encapsulin model was first placed into the map using Chimera. It was then refined against the map by alternating rounds of manual refinem ...	The starting encapsulin model was first placed into the map using Chimera. It was then refined against the map by alternating rounds of manual refinement in Coot and real-space refinement in PHENIX.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	45.5

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	800
Maximum Defocus (nm)	1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	45000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	v3.2.0+210511
IMAGE ACQUISITION	Leginon
CTF CORRECTION	cryoSPARC	v3.2.0+210511
MODEL FITTING	UCSF Chimera	v 1.15
INITIAL EULER ASSIGNMENT	cryoSPARC	v3.2.0+210511
FINAL EULER ASSIGNMENT	cryoSPARC	v3.2.0+210511
RECONSTRUCTION	cryoSPARC	v3.2.0+210511
MODEL REFINEMENT	Coot	0.8.9.1
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		77425

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.