7NTM

ELECTRON MICROSCOPY

Sample

Tetrameric structure of native ADH1 from S. cereviciae in its apo state.

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 222802
Reported Resolution (Å) 2.86
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 BACKBONE TRACE
Refinement Target ?
Overall B Value 123
Fitting Procedure ?
Details Model building and refinement were done using using CCP-EM software suite (Burnley et al, 2017). The X-ray structure of yeast ADH1 (PDB: 5ENV) was used as a starting model for model building. This model was docked into our Cryo-EM map using MolRep (Brown et al, 2014). The resulting starting model was manually adjusted in Coot (Emsley et al, 2010). REFMAC 5 (Brown et al, 2014) used for structure model refinement.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 60
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
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 130000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION Warp 40
IMAGE ACQUISITION EPU 2.7
CTF CORRECTION Warp 40
MODEL FITTING MOLREP ?
INITIAL EULER ASSIGNMENT cryoSPARC v2.15.041
FINAL EULER ASSIGNMENT cryoSPARC v2.15.041
RECONSTRUCTION cryoSPARC v2.15.041
MOLECULAR REPLACEMENT MOLREP ?
MODEL REFINEMENT REFMAC 5
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?