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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