7VFH | pdb_00007vfh

Cryo-EM structure of Vaccinia virus scaffolding protein D13 trimer sextet

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6BEI

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.783
f_angle_d	0.608
f_chiral_restr	0.049
f_plane_restr	0.004
f_bond_d	0.003

Sample
Vaccinia virus scaffolding protein D13 with N-terminal 17 residue truncation, in its trimer sextet oligomeric state

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE-PROPANE
Sample Vitrification Details	3 microliter sample volume was loaded onto a holey grid with additional graphene oxide film. 10 sec waiting time, 5 sec blotting time and blot force 0, no delay time were applied before plunging.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	247311
Reported Resolution (Å)	3.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6BEI)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	2500
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	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND	4.1.9
CTF CORRECTION	RELION	3.1
CTF CORRECTION	cisTEM	1.0.0
MODEL FITTING	UCSF Chimera	1.13.1
MODEL FITTING	Coot	0.9.1
MODEL REFINEMENT	PHENIX	1.18
INITIAL EULER ASSIGNMENT	RELION	3.1
FINAL EULER ASSIGNMENT	cisTEM	1.0.0
CLASSIFICATION	cisTEM	1.0.0
RECONSTRUCTION	cisTEM	1.0.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		303052	D13 trimer sextet images were extracted from the images of tubular assembly (EMD-31953) by symmetry expansion and signal subtraction.