ELECTRON MICROSCOPY

Sample

Dodecameric assembly of DPS-like protein

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Blot force 5 Blot time 4
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 436835
Reported Resolution (Å) 2.37
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 Correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details Workflow involved generating a homology model from 2CLB structure from S. solfataricus with the Pf sequence, using Swiss Model. Then, that homology model was fit to the map density initially in Chimera using fitmap. After that, it was initially refined with rigid body real-space refinement in Phenix, tuned in coot, and subsequently finished refining with flexible fitting and enforced tetrahedral symmetry.
Data Acquisition
Detector Type GATAN K3 (6k x 4k)
Electron Dose (electrons/Å2) 65
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS TALOS
Minimum Defocus (nm) 500
Maximum Defocus (nm) 2200
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.62
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification 36000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details Beam tilt was performed with a 3x3 matrix with corners omitted.
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 3.20
IMAGE ACQUISITION SerialEM 3.8.8
CTF CORRECTION cryoSPARC 3.2
MODEL FITTING UCSF Chimera 1.15
INITIAL EULER ASSIGNMENT cryoSPARC 3.2
FINAL EULER ASSIGNMENT cryoSPARC 3.2
CLASSIFICATION cryoSPARC 3.2
RECONSTRUCTION cryoSPARC 3.2
MODEL REFINEMENT PHENIX 1.19
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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