8FMA

Nodavirus RNA replication proto-crown, detergent-solubliized C11 multimer

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	3.474
f_angle_d	0.372
f_chiral_restr	0.046
f_plane_restr	0.002
f_bond_d	0.001

Sample
Nodavirus RNA replication proto-crown, detergent-solubliized C11 multimer

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	13701
Reported Resolution (Å)	3.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C11

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	The final model includes 22 chains representing 11 protein A polypeptides. Chains A-K represent the N-terminal floor segment built into the high-resol ...	The final model includes 22 chains representing 11 protein A polypeptides. Chains A-K represent the N-terminal floor segment built into the high-resolution EM density. Chains L-V represent a mainchain trace of the polymerase segment rigid body fit into the map and are included to give a more complete picture of the molecule. The polymerase mainchain trace was refined from an Alphafold prediction into a map obtained by symmetry expansion with subtraction. The polymerase map is uploaded as a separate entry. The two segments have separate chain IDs as it is unclear from the density which polymerase connects to which floor segment.

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	100

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
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cisTEM	2.0
IMAGE ACQUISITION	SerialEM	3.8
CTF CORRECTION	cisTEM	2.0
MODEL FITTING	UCSF ChimeraX	1.3
MODEL FITTING	Coot	0.9.8.1
MODEL FITTING	ISOLDE	1.3
INITIAL EULER ASSIGNMENT	cisTEM	2.0
FINAL EULER ASSIGNMENT	cisTEM	2.0
CLASSIFICATION	cisTEM	2.0
RECONSTRUCTION	cisTEM	2.0
MODEL REFINEMENT	PHENIX	1.20.1

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.