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Dictyostelium discoideum HF380 cytoplasmic dynein motor domain in the presence of ADP
Specimen Preparation
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
1347494
Reported Resolution (Å)
2.76
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
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1 (3VKG)
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Real-space target; weighted map sum at atom centers
Overall B Value
113.6
Fitting Procedure
Details
A monomeric HF380 motor-domain model was fitted into cryo-EM map and refined by phenix.real_space_refine.
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
80
Imaging Experiment
1
Date of Experiment
Temperature (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
EM Software
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
MODEL REFINEMENT
PHENIX
1.21_5207
INITIAL EULER ASSIGNMENT
cryoSPARC
4.4.1
FINAL EULER ASSIGNMENT
cryoSPARC
4.4.1
CLASSIFICATION
cryoSPARC
4.4.1
RECONSTRUCTION
cryoSPARC
4.4.1
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.
4072620
Particles were selected by blob picking and template-based picking in cryoSPARC, followed by 2D classification and 3D refinement to retain 4,072,620 particles for 3D variability analysis.