9N6B | pdb_00009n6b

Structure of the retron IA complex with HNH nuclease in the "up" orientation

ELECTRON MICROSCOPY

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	18.977
f_angle_d	0.597
f_chiral_restr	0.042
f_plane_restr	0.006
f_bond_d	0.003

Sample
Retron IA surveillance complex with HNH nuclease bound in the "down" orientation

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	356186
Reported Resolution (Å)	3.09
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Reported resolution from cryoSPARC's GSFSC estimation
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	Alphafold predicted structures of each individual subunit were first rigid body fit in ChimeraX using the fit in map command before initial relaxation ...	Alphafold predicted structures of each individual subunit were first rigid body fit in ChimeraX using the fit in map command before initial relaxation using ISOLDE and final refinement in PHENIX RealSpaceRefinement. COOT was used for manual editing.

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	56.69

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2500
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	45000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286:

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		5915380	Particles picked using a 20 Angstrom lowpass filtered template volume that was produced de novo using blob picked particles

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.