9HXE | pdb_00009hxe

Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 saturated with pdApdG dinucleotide (HEPN active site mutant R502A)

ELECTRON MICROSCOPY

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Starting Model(s)

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

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.8421
f_angle_d	0.7124
f_chiral_restr	0.0522
f_plane_restr	0.0054
f_bond_d	0.0044

Sample
Bacterial antiviral defense protein Ec2ApeA from Escherichia coli strain 2-156-04_S4_C1 saturated with pdApdG dinucleotide (HEPN active site mutant R502A)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	61743
Reported Resolution (Å)	3.2
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	D5

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	30

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS GLACIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	92000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4.5.3

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