ELECTRON MICROSCOPY

Sample

A8B8 photosynthetic glyceraldeyde 3-phospahte dehydrogenase hetero-hexadecamer (major conformer) complexed with NAD

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Vitrification carried out in conventional atmosphere.
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 55141
Reported Resolution (Å) 3.1
Resolution Method FSC 0.143 CUT-OFF
Other Details RELION was used for the reconstruction.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol RIGID BODY FIT
Refinement Target Cross-correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details Initial local fitting was done unsing ChimeraX starting from the crystallographic model PDB ID 2PKQ. Refinement was obtained trough several iterative cycles of Coot manual adjustment and Phenix real space refinement.
Data Acquisition
Detector Type FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å2) 40
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS KRIOS
Minimum Defocus (nm) 1500
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 ?
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details Preliminary grid screening was perfomed manually on a FEI Tecnai G2 F20 TEM equipped with cryo-box and direct electron detector.
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION RELION 4.0
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION CTFFIND 4.1
MODEL FITTING UCSF ChimeraX 1.7
MODEL REFINEMENT PHENIX 1.20
RECONSTRUCTION RELION 4.0
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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