ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.183
f_angle_d0.477
f_chiral_restr0.041
f_plane_restr0.003
f_bond_d0.002
Sample
MVV cleaved synaptic complex intasome
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsCryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles147860
Reported Resolution (Å)3.46
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCC
Overall B Value262
Fitting Procedure
DetailsThe 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 TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)43.6
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TALOS ARCTICA
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification45000
Calibrated Magnification54347
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging DetailsThe stage was tilted to 40 degrees during data collection to account for the preferential orientation of the sample within the vitreous ice.
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.0
IMAGE ACQUISITIONLeginon
CTF CORRECTIONcryoSPARC3.0
MODEL FITTINGPHENIXdev-4213-000
INITIAL EULER ASSIGNMENTcryoSPARC3.0
FINAL EULER ASSIGNMENTcryoSPARC3.0
RECONSTRUCTIONcryoSPARC3.0
MODEL REFINEMENTCoot
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION926176