5MUU

dsRNA bacteriophage phi6 nucleocapsid

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.533
f_angle_d	1.003
f_chiral_restr	0.05
f_bond_d	0.009
f_plane_restr	0.004

Sample
Pseudomonas phage phi6

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	13291
Reported Resolution (Å)	4
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I
Space Group Name	P 1
Length a	1
Length b	1
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1 (4K7H)	2	3
Refinement Space	REAL	REAL
Refinement Protocol	RIGID BODY FIT	AB INITIO MODEL	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details	The structure of P1 was fitted in the map using COOT as a rigid body in two different positions corresponding to subunits P1A and P1B. P1A and P1B mai ...	The structure of P1 was fitted in the map using COOT as a rigid body in two different positions corresponding to subunits P1A and P1B. P1A and P1B main-chains and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints.	The structure of P8 (L3 to Y147) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. Structure was r ...	The structure of P8 (L3 to Y147) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints.	The structure of P4 C-terminus (R292 to L332) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. St ...	The structure of P4 C-terminus (R292 to L332) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	0.73

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)
Maximum Defocus (nm)	300
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	OTHER
Nominal Magnification	160000
Calibrated Magnification	37037
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	ETHAN	1.2
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	CTFFIND	3
CTF CORRECTION	RELION	1.3
MODEL FITTING	Coot	0.8.7
INITIAL EULER ASSIGNMENT	RELION	1.3
FINAL EULER ASSIGNMENT	RELION	1.3
CLASSIFICATION	RELION	1.3
RECONSTRUCTION	RELION	1.3
MODEL REFINEMENT	Coot	0.8.7
MODEL REFINEMENT	PHENIX	1.10.1_2155
MODEL FITTING	Coot	0.8.7
MODEL REFINEMENT	Coot	0.8.7
MODEL REFINEMENT	PHENIX	1.10.1_2155
MODEL FITTING	Coot	0.8.7
MODEL REFINEMENT	Coot	0.8.7
MODEL REFINEMENT	PHENIX	1.10.1_2155

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		16466

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.