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Cryo-EM structure of the freshwater actinorhodopsin, Rhodoluna lacicola (RlActR)
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
Other
Sample
Pentamer of the actinorhodopsin
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
In brief, grids were incubated for 30 seconds, and excess liquid blotted off for 5 seconds applying a blotting force of -6 at 4 degrees and a relative ...
In brief, grids were incubated for 30 seconds, and excess liquid blotted off for 5 seconds applying a blotting force of -6 at 4 degrees and a relative humidity of about 100% before plunging into liquid ethane (-177 degrees to -171 degrees).
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
184961
Reported Resolution (Å)
2.84
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C5
Map-Model Fitting and Refinement
Id
1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Shiff base bond created between K234 and RETINAL (RET)
Data Acquisition
Detector Type
TFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)
1.01
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
1000
Maximum Defocus (nm)
2200
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
165000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
crYOLO
1.5
IMAGE ACQUISITION
SerialEM
CTF CORRECTION
Gctf
1.6
MODEL FITTING
UCSF Chimera
1.7.1
INITIAL EULER ASSIGNMENT
RELION
4
FINAL EULER ASSIGNMENT
cryoSPARC
CLASSIFICATION
RELION
4
RECONSTRUCTION
cryoSPARC
MODEL REFINEMENT
PHENIX
1.20-4459
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
431658
a non-template-driven convolutional neural network (CNN) based-particle picking was performed within CrYOLO (version 1.5). A total of 431,658 particles were selected with the pre-trained general model and extracted from the remaining 8170 dose-weighted micrographs with Relion4