7YZ4

ELECTRON MICROSCOPY

Sample

Free form of mouse somatic dicer

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Described in STAR methods
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 92906
Reported Resolution (Å) 3.84
Resolution Method FSC 0.143 CUT-OFF
Other Details The map resolution was further improved up to 3.47 with local refinement of the individual protein domains.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target Ramachandran Plot, Rotamer Analysis, Density Analysis
Overall B Value 87.8
Fitting Procedure ?
Details Endoribonuclease mouse Dicer from AlphaFold database was used as initial model. Initial local fitting into combined map from locally refined protein parts was done using Chimera and then Coot's Real Space Refine Zone.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 55
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 800
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 ?
Imaging Experiment
Task Software Package Version
CTF CORRECTION cryoSPARC v3.3.1
MODEL FITTING UCSF Chimera 1.15
CLASSIFICATION cryoSPARC v3.3.1
RECONSTRUCTION cryoSPARC v3.3.1
MODEL REFINEMENT Coot 0.9.6
MODEL REFINEMENT PHENIX 1.19.2-4158
MODEL REFINEMENT ISOLDE 1.1.0
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?