Experiment: 27PT

Dictyostelium discoideum cytoplasmic dynein motor domain in complex with ADP.Vi (Phi-particle)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VKG

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	5.954
f_angle_d	0.46
f_chiral_restr	0.038
f_plane_restr	0.004
f_bond_d	0.002

Sample
Dictyostelium discoideum HF380 cytoplasmic dynein motor domain in the presence of ATP and orthovanadate

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	1378380
Reported Resolution (Å)	2.2
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The final non-uniform refinement was performed with C2 symmetry imposed.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

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	62
Fitting Procedure
Details	A monomeric HF380 motor-domain model was fitted into the C2-reconstructed 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
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.	1755826	Particles were selected by blob picking and template-based picking in cryoSPARC. After 2D classification, 1,755,826 particles with well-defined secondary-structure features were extracted with a 600-pixel box.