7NO0

Structure of the mature RSV CA lattice: T=1 CA icosahedron

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.425
f_angle_d	0.677
f_chiral_restr	0.043
f_bond_d	0.005
f_plane_restr	0.004

Sample
Rous sarcoma virus - Prague C

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	blot time= 2.5 s blot force= 0

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	20498
Reported Resolution (Å)	3.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (3TIR)
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details	The CANTD and CACTD of one CA monomer of pdb 3TIR were independently placed into the EM-density using the rigid body fitting option in UCSF Chimera. Subsequently the linker connecting the two CA domains was joined in Coot. To account for the different monomer-monomer interactions in the RSV CA pentamer, the monomers were replicated according to the inherent 5-fold symmetry of the map and an additional ring of CACTDs was rigid-body fitted into the EM-densities of the surrounding CA pentamers. A map segment (defined by a mask extending 3 Angstrom around the rigid body fitted model) was extracted, and real-space coordinate refinement against the EM-density was performed using Phenix. This was iterated with manual model building in Coot, similar as described previously. In brief, secondary structure restraints and non-crystallographic symmetry (NCS) restraints were applied throughout all refinements. Each Phenix iteration consisted of 5 macro cycles, in which simulated annealing was performed in every macro cycle. Atomic displacement parameter (ADP) refinement was per formed at the end of each iteration.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TECNAI ARCTICA
Minimum Defocus (nm)	800
Maximum Defocus (nm)	1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	63000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

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

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	CTF estimation and correction was performed using GCTF in the RELION wrapper	150599	2394 micrographs were taken, from which 374 particles were manually picked and 2D classified to generate templates for auto-picking. Two rounds of auto-picking and 2D classification resulted in 150599 extracted particles.