5U1C
Structure of tetrameric HIV-1 Strand Transfer Complex Intasome
ELECTRON MICROSCOPY
Sample |
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complex formed by a tetrameric assembly of Sso7d-fusion HIV-1 Integrase with the product of DNA strand transfer |
Specimen Preparation | |
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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 ... |
3D Reconstruction | |
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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 | |||||
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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 ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 95 |
Imaging Experiment | 1 |
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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 | ||
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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 | ||||
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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 |