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MVV cleaved synaptic complex (CSC) intasome at 3.4 A resolution
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
12.183
f_angle_d
0.477
f_chiral_restr
0.041
f_plane_restr
0.003
f_bond_d
0.002
Sample
MVV cleaved synaptic complex intasome
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
HOMEMADE PLUNGER
Cryogen Name
ETHANE
Sample Vitrification Details
Cryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
147860
Reported Resolution (Å)
3.46
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C2
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
CC
Overall B Value
262
Fitting Procedure
Details
The STC model refined in study, with the tDNA removed, was docked into the CSC cryoEM map using UCSF Chimera. It was observed that there were some sli ...
The STC model refined in study, with the tDNA removed, was docked into the CSC cryoEM map using UCSF Chimera. It was observed that there were some slight differences in some domain positions, to address this, individual domains that were not well fitted to the map were docked as individual domains to achieve a best-fit starting model. Two (C2 related) NTDs (aa 1-35) were removed from the model due to lack of supporting map. Adjustments were made to the model interactively using Coot and the coordinates were subjected to real-space refinement in Phenix dev-4213-000 employing C2 NCS constraints.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
43.6
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TALOS ARCTICA
Minimum Defocus (nm)
1000
Maximum Defocus (nm)
3000
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
54347
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
The stage was tilted to 40 degrees during data collection to account for the preferential orientation of the sample within the vitreous ice.