Experiment: 3J94

Structure of ATP-bound N-ethylmaleimide sensitive factor determined by single particle cryoelectron microscopy

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NSF

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.409
f_angle_d	1.762
f_chiral_restr	0.071
f_bond_d	0.008
f_plane_restr	0.006

Sample
ATP-bound N-ethylmaleimide sensitive factor

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK I
Cryogen Name	ETHANE
Sample Vitrification Details	Blot for 3.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	50781
Reported Resolution (Å)	4.2
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Every image is the sum of 30 frames recorded using the K2 Summit. The final reconstruction was calculated from images summed from frames #2-#18. (Sing ...	Every image is the sum of 30 frames recorded using the K2 Summit. The final reconstruction was calculated from images summed from frames #2-#18. (Single particle details: 3D classification, refinement, and reconstruction were performed using RELION) (Single particle--Applied symmetry: C1)
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (1NSF)
Refinement Space	RECIPROCAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	R-factor
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--flexible DETAILS--D2 domain was from crystal structure 1NSF. D1 domain was built de novo.

Data Acquisition
Detector Type	GATAN K2 (4k x 4k)
Electron Dose (electrons/Å**2)	26.4

Imaging Experiment	1
Date of Experiment	2014-02-28
Temperature (Kelvin)
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)	-1800
Maximum Defocus (nm)	-2800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.3
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	OTHER
Nominal Magnification	31000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	PHENIX
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	RELION

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	Each particle