ELECTRON MICROSCOPY

Sample

Ternary complex of NAD+ and human PARP4 bound to oligomerized human MVP

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Vitrification carried out under standard conditions
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 93859
Reported Resolution (Å) 2.9
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details The starting model was the rat homologue of MVP from a previous crystal structure of the vault cage (PDB accession no 4V60). Small molecule coordinates were retrieved from the REFMAC monomer library in COOT. The final model was refined in real space and validated using PHENIX
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 45
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 700
Maximum Defocus (nm) 1700
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 0.01
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification 53000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details Preliminary grid screening was performed manually.
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 4.4
IMAGE ACQUISITION SerialEM 4.0
CTF CORRECTION cryoSPARC 4.4
MODEL FITTING Coot 0.8.9.2
INITIAL EULER ASSIGNMENT cryoSPARC 4.4
FINAL EULER ASSIGNMENT cryoSPARC 4.4
CLASSIFICATION cryoSPARC 4.4
RECONSTRUCTION cryoSPARC 4.4
MODEL REFINEMENT PHENIX 1.12
MODEL FITTING Coot 0.8.9.2
MODEL REFINEMENT PHENIX 1.12
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION CTF correction was performed when movies were imported into cryoSPARC Live