7PHM | pdb_00007phm

Cryo-EM structure of Mycobacterium tuberculosis encapsulin

ELECTRON MICROSCOPY

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Sample
Empty encapsulin nanocompartment

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	1000000
Reported Resolution (Å)	2.2
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Correlation coefficient
Overall B Value
Fitting Procedure
Details	Model was generated ab initio using Buccaneer within the CCPEM package and manually corrected using Coot before being refined using Isolde within ChimeraX and Phenix Real Space Refinement within the CCPEM package.

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	45

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	2000
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
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	3.1.1
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND	4.1
MODEL FITTING	UCSF Chimera	1.12
INITIAL EULER ASSIGNMENT	RELION	3.1.1
FINAL EULER ASSIGNMENT	RELION	3.1.1
CLASSIFICATION	RELION	3.1.1
RECONSTRUCTION	RELION	3.1.1
MODEL REFINEMENT	ISOLDE	1.2
MODEL REFINEMENT	PHENIX	1.13

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		2000000	2D class averages were produced using Relion from 1000 manually-picked particles. These were then used as picking templates.