Experiment: 9DIG

Rous sarcoma virus frameshifting pseudoknot RNA EM straight dimer

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9DIB

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.888
f_angle_d	0.758
f_chiral_restr	0.034
f_bond_d	0.007
f_plane_restr	0.004

Sample
Dimeric RNA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK I
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	88523
Reported Resolution (Å)	3.22
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (9DIB)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	Cross-correlation coefficient
Overall B Value	116.7
Fitting Procedure
Details	Phenix real-space refinement, using real-space refinement, simulated annealing on the first step, B-factor, occupancy, and global minimization with NC ...	Phenix real-space refinement, using real-space refinement, simulated annealing on the first step, B-factor, occupancy, and global minimization with NCS and secondary structure restraints

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	54.4

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2000
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
PARTICLE SELECTION	Topaz
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	CTFFIND	4.1
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC
CLASSIFICATION	RELION
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		3400000