ELECTRON MICROSCOPY

Sample

Native purified Pol II elongation complex from Drosophila melanogaster without the Rpb4/Rpb7 stalk

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 96409
Reported Resolution (Å) 3.37
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space ?
Refinement Protocol AB INITIO MODEL
Refinement Target ?
Overall B Value 50
Fitting Procedure ?
Details The model was based on PDB: 6GML. First, 6GML was rigid-body fit in the cryo-EM Coulomb potential density map using UCSF ChimeraX. Next, AlphaFold2 models for individual Drosophila melanogaster Pol II subunits were aligned to their 6GML counterparts, and further optimized in the density using rigid-body fit. For the final model optimization, phenix.real_space_refine was used
Data Acquisition
Detector Type FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å2) 50.65
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS TALOS
Minimum Defocus (nm) 1000
Maximum Defocus (nm) 2500
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification ?
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 4.3.1
IMAGE ACQUISITION EPU 3.4
CTF CORRECTION cryoSPARC 4.3.1
MODEL FITTING UCSF ChimeraX 1.8
MODEL REFINEMENT Coot 0.9.8.7
MODEL REFINEMENT PHENIX 1.21.5207
INITIAL EULER ASSIGNMENT cryoSPARC 4.3.1
FINAL EULER ASSIGNMENT cryoSPARC 4.3.1
RECONSTRUCTION cryoSPARC 4.3.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION 'Patch CTF Estimation' in cryoSPARC