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Two-subunit asymmetric unit of Epstein-Barr virus annealase BALF2 ssDNA-annealing complex
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
4.61
f_angle_d
0.521
f_chiral_restr
0.041
f_plane_restr
0.005
f_bond_d
0.003
Sample
Asymmetric subunit of the BALF2 ssDNA-annealing filament
Specimen Preparation
Sample Aggregation State
FILAMENT
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
557352
Reported Resolution (Å)
2.2
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Though C2 symmetry was applied to the map, the actual structure is not C2. This is primarily because of differences in the DNA sequences. The actual D ...
Though C2 symmetry was applied to the map, the actual structure is not C2. This is primarily because of differences in the DNA sequences. The actual DNA sequences bound to each subunit are different between particles and are lost during particle averaging. Different sequences were built in to the density based on areas of highest complementarity of the substrate.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C2
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Initial fitting was done in isolde before refinement in Phenix.
Though C2 symmetry was applied to the map, the actual structure is not C2. This is pr ...
Initial fitting was done in isolde before refinement in Phenix.
Though C2 symmetry was applied to the map, the actual structure is not C2. This is primarily because of differences in the DNA sequences. The actual DNA sequences bound to each subunit are different between particles and are lost during particle averaging. Different sequences were built in to the density based on areas of highest complementarity of the substrate.