ELECTRON MICROSCOPY

Sample

Dictyostelium discoideum HF380 cytoplasmic dynein motor domain in the absence of nucleotide

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 910656
Reported Resolution (Å) 2.66
Resolution Method FSC 0.143 CUT-OFF
Other Details The selected particles were refined by non-uniform refinement in cryoSPARC.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target Real-space target; weighted map sum at atom centers
Overall B Value 92.3
Fitting Procedure ?
Details A monomeric HF380 motor-domain model was fitted into the cryo-EM map and refined by phenix.real_space_refine.
Data Acquisition
Detector Type GATAN K3 (6k x 4k)
Electron Dose (electrons/Å2) 80
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model JEOL CRYO ARM 300
Minimum Defocus (nm) 700
Maximum Defocus (nm) 2200
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.7
Imaging Mode BRIGHT FIELD
Specimen Holder Model JEOL CRYOSPECPORTER
Nominal Magnification 60000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 4.4.1
IMAGE ACQUISITION SerialEM 3.8 or 4.050
CTF CORRECTION cryoSPARC 4.4.1
MODEL FITTING UCSF ChimeraX 1.7
MODEL FITTING Coot 0.9.8.92
INITIAL EULER ASSIGNMENT cryoSPARC 4.4.1
FINAL EULER ASSIGNMENT cryoSPARC 4.4.1
CLASSIFICATION cryoSPARC 4.4.1
RECONSTRUCTION cryoSPARC 4.4.1
MODEL REFINEMENT PHENIX 1.21_5207
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION CTF parameters were estimated using Patch CTF estimation in cryoSPARC and further refined by global and local CTF refinement.
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