9BI0

Streptomyces griseus Family 2B encapsulin shell with 2-methylisoborneol synthase cargo in 20 mM cAMP

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	Q54255

Sample
Streptomyces griseus Family 2B encapsulin shell with 2-methylisoborneol synthase cargo in 20 mM cAMP
Sample Components
2-Methylisoborneol synthase cargo protein

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	9170
Reported Resolution (Å)	2.93
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Homogeneous refinement was performed with I symmetry, per-particle defocus optimization, per-group CTF parameterization, spherical aberration fit, tet ...	Homogeneous refinement was performed with I symmetry, per-particle defocus optimization, per-group CTF parameterization, spherical aberration fit, tetrafoil fit, anisotropic magnification fit, and Ewald sphere correction with a positive curvature sign.
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	cross-correlation coefficient
Overall B Value	92
Fitting Procedure
Details	An AlphaFold-generated model was fit into the map using ChimeraX v1.5. The model was then refined iteratively by alternating rounds of manual refineme ...	An AlphaFold-generated model was fit into the map using ChimeraX v1.5. The model was then refined iteratively by alternating rounds of manual refinement in Coot v8.9.1 and real-space refinements using PHENIX v1.20.1-4487.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	39.98

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	4.4.0+231114
IMAGE ACQUISITION	Leginon
CTF CORRECTION	cryoSPARC	4.4.0+231114
MODEL FITTING	UCSF ChimeraX	1.5
INITIAL EULER ASSIGNMENT	cryoSPARC	4.4.0+231114
FINAL EULER ASSIGNMENT	cryoSPARC	4.4.0+231114
RECONSTRUCTION	cryoSPARC	4.4.0+231114
MODEL REFINEMENT	Coot	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

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.