5U1C | pdb_00005u1c

Structure of tetrameric HIV-1 Strand Transfer Complex Intasome

ELECTRON MICROSCOPY

Sample
complex formed by a tetrameric assembly of Sso7d-fusion HIV-1 Integrase with the product of DNA strand transfer

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	Sample containing HIV STC intasomes in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey gold UltrAuF ...	Sample containing HIV STC intasomes in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey gold UltrAuFoil grids (Quantifoil), adsorbed for 30 seconds, then plunged into liquid ethane using a manual cryo-plunger in an ambient environment of 4 degrees C.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	83766
Reported Resolution (Å)	3.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Resolution-limited refinement used throughout
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	FSC 0.5
Overall B Value	180
Fitting Procedure
Details	To generate ensemble models, the complete intasome model was iteratively relaxed - using two-fold symmetry and a combination of Rosetta and Phenix - a ...	To generate ensemble models, the complete intasome model was iteratively relaxed - using two-fold symmetry and a combination of Rosetta and Phenix - against one half map (the working map) and inspected for consistency with the second half map (the free map). The model was then adjusted manually using Coot. Final ensemble modeling used half maps for all aspects of refinement and evaluation: 500 models were generated as described using Rosetta. From the 100 top-scoring models (scored by Rosetta energy), the ten models with the best map-to-model FSC were selected and refined in real space using secondary-structure restraints in Phenix. Molprobity was used throughout the refinement process.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	95

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
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
IMAGE ACQUISITION	Leginon	3.2
CTF CORRECTION	CTFFIND	3
MODEL FITTING	Rosetta	2015.12.57698_bundle
MODEL FITTING	PHENIX	2499
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	RELION	1.3
FINAL EULER ASSIGNMENT	FREALIGN	9.11
CLASSIFICATION	FREALIGN	3.11
RECONSTRUCTION	FREALIGN	9.11
MODEL REFINEMENT	PHENIX	2499
MODEL REFINEMENT	Coot

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	performed internally in Relion and Frealign	274764

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.