ELECTRON MICROSCOPY

Sample

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

Specimen Preperation
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 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
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 - 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/Å2) 95
Imaging Experiment
Date of Experiment ?
Temprature (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 ?
Imaging Experiment
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
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