3JCA

Core model of the Mouse Mammary Tumor Virus intasome


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CZ1 
experimental modelPDB 5CZ2 
experimental modelPDB 5D7U 
Sample
Mouse Mammary Tumor Virus intasome complex
Sample Components
betaretroviral integrase
MMTV U5 DNA end
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsSample 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 MethodSINGLE PARTICLE
Number of Particles30307
Reported Resolution (Å)4.8
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsLocal 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 TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1 (5CZ1, 5CZ2, 5D7U)
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement TargetFSC, Rosetta energy
Overall B Value300
Fitting Procedure
DetailsREFINEMENT 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 TypeGATAN K2 (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment2015-04-15
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification22500
Calibrated Magnification38167
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGRosetta
RECONSTRUCTIONFREALIGN
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
each particle