CryoEM reconstruction of integrase filament at the lumen of native HIV-1 cores (box size 34.2 nm)
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 10.969 |
| f_angle_d | 0.481 |
| f_chiral_restr | 0.04 |
| f_plane_restr | 0.004 |
| f_bond_d | 0.002 |
| Sample |
|---|
| Human immunodeficiency virus 1 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA PLUNGER |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | |
| Embedding Material | vitreous ice |
| Embedding Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 58103 |
| Reported Resolution (Å) | 4.63 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1K6Y, 9C9M, 8A1P, 2B4J, 6SKK) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 49.6 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1500 |
| Maximum Defocus (nm) | 3500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Topaz | |
| PARTICLE SELECTION | Gautomatch | |
| IMAGE ACQUISITION | EPU | |
| MODEL FITTING | UCSF Chimera | |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.6.2 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.6.2 |
| CLASSIFICATION | cryoSPARC | 4.6.2 |
| RECONSTRUCTION | cryoSPARC | 4.6.2 |
| MODEL REFINEMENT | PHENIX | 1.21.2_5419 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
