7U32

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.

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	3.0
IMAGE ACQUISITION	Leginon
CTF CORRECTION	cryoSPARC	3.0
MODEL FITTING	PHENIX	dev-4213-000
INITIAL EULER ASSIGNMENT	cryoSPARC	3.0
FINAL EULER ASSIGNMENT	cryoSPARC	3.0
RECONSTRUCTION	cryoSPARC	3.0
MODEL REFINEMENT	Coot

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		926176

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.