3JCA

Core model of the Mouse Mammary Tumor Virus intasome

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CZ1
experimental model	PDB	5CZ2
experimental model	PDB	5D7U

Sample
Mouse Mammary Tumor Virus intasome complex
Sample Components
betaretroviral integrase
MMTV U5 DNA end

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	Sample containing MMTV intasomes in SEC buffer (to which the detergent NP-40 was added to a final concentration of 0.05%) was applied onto a freshly p ...	Sample containing MMTV intasomes in SEC buffer (to which the detergent NP-40 was added to a final concentration of 0.05%) was applied onto a freshly plasma-treated (6s, Gatan Solarus plasma cleaner) holey carbon C-flat grid (CF-1.2/1.3-4C, Protochips, Inc.), allowing the sample to adsorb for 30 seconds and then plunge-freezing in liquid ethane using a manual cryo-plunger in an ambient environment of 4 degrees C.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	30307
Reported Resolution (Å)	4.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Local FSC values range from 4-5 A. (Single particle details: IN-NTD and IN-CCD domains of flanking INs 5-8 were computationally removed using Relion a ...	Local FSC values range from 4-5 A. (Single particle details: IN-NTD and IN-CCD domains of flanking INs 5-8 were computationally removed using Relion after assignment of Euler angles to full octameric particles and masking out of flanking regions.) (Single particle - Applied symmetry: C2)
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (5CZ1, 5CZ2, 5D7U)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	FSC, Rosetta energy
Overall B Value	300
Fitting Procedure
Details	REFINEMENT PROTOCOL--real-space refinement DETAILS--Initial components solved by X-ray were rigid-body docked. Linker regions were built de novo from ...	REFINEMENT PROTOCOL--real-space refinement DETAILS--Initial components solved by X-ray were rigid-body docked. Linker regions were built de novo from the EM density. The full model was refined using real-space methods in Rosetta.

Data Acquisition
Detector Type	GATAN K2 (4k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment	2015-04-15
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	4000
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	22500
Calibrated Magnification	38167
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	Rosetta
RECONSTRUCTION	FREALIGN

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	each particle

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 R01GM157729.