9UCZ | pdb_00009ucz

Cryo-EM structure of the R2Tg retrotransposon in complex with R2RNA and rDNA in the initiating target-primed reverse transcription state (ZF3/2 disordered)

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
s_dihedral_angle_6_deg	14.7669
s_dihedral_angle_3_deg	11.2249
s_dihedral_angle_1_deg	5.63
s_dihedral_angle_2_deg	3.4277
s_angle_nonh_deg	1.3853
s_nbtor	0.2065
s_nbd	0.1873
s_metal_ion	0.1616
s_hbond_nbd	0.1415
s_chiral_restr	0.0513
s_planes	0.0055
s_bond_nonh_d	0.0054

Sample
R2Tg-R2RNA-28SDNA ternary complex

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	441626
Reported Resolution (Å)	2.61
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	49.6

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	1800
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
CTF CORRECTION	cryoSPARC
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC
CLASSIFICATION	cryoSPARC
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	Servalcat

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