9B9I | pdb_00009b9i

Myxococcus xanthus EncA encapsulin engineered pore mutant with T=1 icosahedral symmetry

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7S21

Sample
Myxococcus xanthus EncA encapsulin engineered pore mutant with T=1 icosahedral symmetry

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	61808
Reported Resolution (Å)	2.86
Resolution Method	FSC 0.143 CUT-OFF
Other Details	CryoSPARC homogeneous refinement was performed with I symmetry, per-particle defocus optimization, per-group CTF-parameterization, and Ewald sphere co ...	CryoSPARC homogeneous refinement was performed with I symmetry, per-particle defocus optimization, per-group CTF-parameterization, and Ewald sphere correction enabled.
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (7S21)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	cross-correlation coefficient
Overall B Value	126.4
Fitting Procedure
Details	ChimeraX v1.2.5 was first used to place the starting model (PDB: 7S21) in the cryo-EM map by using the fit in map command. The model was then manually ...	ChimeraX v1.2.5 was first used to place the starting model (PDB: 7S21) in the cryo-EM map by using the fit in map command. The model was then manually refined using Coot v 0.9.8.1, followed by iterative real-space refinements in Phenix v1.20.1-4487-000. BioMT operators were identified from the cryo-EM map using map_symmetry command in Phenix then applied to the model using the apply_ncs command to assemble the complete shell. Real-space refinement was repeated in Phenix with NCS constraints applied. The BioMT operators were then identified using find_ncs command in Phenix and applied to the header of a protomer of the NCS-refined model.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	39.18

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TECNAI ARCTICA
Minimum Defocus (nm)	1000
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	3.10.0
IMAGE ACQUISITION	Leginon
CTF CORRECTION	cryoSPARC	3.10.0
MODEL FITTING	UCSF ChimeraX	1.2.5
INITIAL EULER ASSIGNMENT	cryoSPARC	3.10.0
FINAL EULER ASSIGNMENT	cryoSPARC	3.10.0
RECONSTRUCTION	cryoSPARC	3.10.0
MODEL REFINEMENT	PHENIX	v1.20.1-4487-000
MODEL REFINEMENT	Coot	v0.9.8.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		66813

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.