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Mammalian Dicer in the "pre-dicing state" with pre-miR-15a substrate
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
13.029
f_angle_d
0.794
f_chiral_restr
0.046
f_plane_restr
0.011
f_bond_d
0.004
Sample
Pre-dicing state of mouse somatic dicer with pre-mir-15a
Sample Components
Pre-dicing state of mouse somatic dicer
pre-mir-15a
Specimen Preparation
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
154665
Reported Resolution (Å)
4.19
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
Id
1
2
3
Refinement Space
REAL
REAL
REAL
Refinement Protocol
FLEXIBLE FIT
FLEXIBLE FIT
FLEXIBLE FIT
Refinement Target
Ramachandran Plot, Rotamer Analysis, Density Analysis
Correlation coefficient
Ramachandran Plot, Rotamer Analysis, Clash Score
Overall B Value
134.8
134.8
134.8
Fitting Procedure
Details
Endoribonuclease mouse Dicer from AlphaFold database was used as initial model. Initial local fitting was done using Chimera and then Coot's Real Spac ...
Endoribonuclease mouse Dicer from AlphaFold database was used as initial model. Initial local fitting was done using Chimera and then Coot's Real Space Refine Zone.
PHENIX Real-space refinement was used for flexible fitting.
ISOLDE was used for flexible fitting with torsion restraints defined for polypeptide and distance restraints for polyribonucleotide chain.