6TFJ | pdb_00006tfj

Vip3Aa protoxin structure

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.1123
f_angle_d	0.4078
f_chiral_restr	0.0393
f_plane_restr	0.0023
f_bond_d	0.002

Sample
Vip3Aa protoxin

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	478797
Reported Resolution (Å)	2.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details	The atomic coordinates were manually modeled de novo in the cryo-EM map using Coot, and then subjected to iterative rounds of real space refinement using Phenix

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	56.6

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	EPU
CTF CORRECTION	Gctf
CTF CORRECTION	RELION	3.0
INITIAL EULER ASSIGNMENT	RELION	3.0
FINAL EULER ASSIGNMENT	RELION	3.0
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	PHENIX	1.17

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION