Experiment: 8EDG

Cryo-EM structure of the Hermes transposase bound to two left-ends of its DNA transposon

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6DX0
experimental model	PDB	4D1Q
experimental model	PDB	8EB5

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	24.804
f_angle_d	0.574
f_chiral_restr	0.038
f_plane_restr	0.004
f_bond_d	0.003

Sample
Two left-end Hermes transpososome

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	143400
Reported Resolution (Å)	4.64
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The 3D reconstruction is not representative of the complex in solution. The Hermes transposase forms a tetramer of dimers assembled in a ring like sha ...	The 3D reconstruction is not representative of the complex in solution. The Hermes transposase forms a tetramer of dimers assembled in a ring like shape. Due to their low resolution two Hermes dimers have been partially or completely masked out during the processing. Only the opposite two Hermes dimers interacting with the DNAs have been fully reconstructed, along with the two DNAs and the two BED domains of a third Hermes dimer.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6DX0, 4D1Q, 8EB5)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	22.3

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS GLACIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	crYOLO
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	RELION	3.1
MODEL FITTING	UCSF Chimera	1.13.1
MODEL FITTING	Coot	0.9
MODEL REFINEMENT	PHENIX	1.19.2
INITIAL EULER ASSIGNMENT	RELION	3.1
FINAL EULER ASSIGNMENT	RELION	3.1
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	RELION	3.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		3850000