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 ... |
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 |