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Structure of the Macrobrachium rosenbergii Nodavirus
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
8.816
f_angle_d
0.843
f_chiral_restr
0.059
f_bond_d
0.007
f_plane_restr
0.004
Sample
Macrobrachium rosenbergii nodavirus
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
Cryogen Name
ETHANE
Sample Vitrification Details
VLPs were deposited onto a continuous carbon film that had been floated onto a quantifoil holey carbon film (R2/2)
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
40883
Reported Resolution (Å)
3.28
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Standard Relion workflow for icosahedral particle.
Refinement Type
Symmetry Type
POINT
Point Symmetry
I
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
Overall B Value
140
Fitting Procedure
Details
Model built largely ab initio, following docking of a homology model based on PDB 4LLF. The homology model matched in two strands at residues - 104-13 ...
Model built largely ab initio, following docking of a homology model based on PDB 4LLF. The homology model matched in two strands at residues - 104-135 and 232-243. This served as the starting point for manual model building. The model was then subjected to real space refinement using Phenix.