7YYN
Mammalian Dicer in the dicing state with pre-miR-15a substrate
ELECTRON MICROSCOPY
Sample |
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Dicing state of mouse oocyte dicer with pre-miR-15a |
Sample Components |
59-nt precursor of miR-15a |
Isoform 2 of Endoribonuclease Dicer |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | Described in STAR methods |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 84697 |
Reported Resolution (Å) | 6.21 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
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Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | Correlation coefficient | ||||
Overall B Value | 451.4 | ||||
Fitting Procedure | |||||
Details | Initial model for mouse oocyte Dicer was calculated using AlphaFold 2.0. Initial rigid body fitting was done using Chimera. Further refinement was don ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 55 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 3500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | crYOLO | 1.7.5 |
CTF CORRECTION | cryoSPARC | v3.3.1 |
MODEL FITTING | UCSF ChimeraX | 1.15 |
CLASSIFICATION | cryoSPARC | v3.3.1 |
RECONSTRUCTION | cryoSPARC | v3.3.1 |
MODEL REFINEMENT | ISOLDE | 1.1.0 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 230362 |