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Rhodospirillum rubrum Nitrogenase-like Methylthio-alkane Reductase Complex with an Oxidized P-cluster
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Sample
Complex of marDK heterotetramer under dithionite reduced conditions
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3.5ul sample was applied to a glow discharged UltrAuFoil grid, blotted for 3 or 4 seconds before plunged in liquid ethane cooled with liquid nitrogen. ...
3.5ul sample was applied to a glow discharged UltrAuFoil grid, blotted for 3 or 4 seconds before plunged in liquid ethane cooled with liquid nitrogen.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
149015
Reported Resolution (Å)
2.35
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Final step was actually Non-uniform Refinement of two classes of an Ab Initio reconstruction.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C2
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)
50
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
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
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
105000
Calibrated Magnification
109454
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
Sample was screened using negative staining and Cryo-EM on a screening microscope for sample readiness assessment before automated high-throughput and high-resolution data collection on Titan Krios. Multiple batches of Cryo-EM specimen were prepared in order to deal with the orientation preference.
The calibrated minimum/maximum defocus were the calculated minimum and maximum of images that with contaminants or broken ice.