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Human RAD51B-RAD51C-RAD51D-XRCC2 (BCDX2) complex, 3.4 A resolution
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
4.7375
f_angle_d
0.4973
f_chiral_restr
0.0423
f_plane_restr
0.0028
f_bond_d
0.0023
Sample
RAD51B-RAD51C-RAD51D-XRCC2 (BCDX2)
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
87572
Reported Resolution (Å)
3.4
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Map was enhanced using DeepEMhancer
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
AlphaFold2 monomer predictions of RAD51B, RAD51C, RAD51D and XRCC2 were docked into the EM density using Dock and Rebuild in Phenix. ATP and Mg2+ were ...
AlphaFold2 monomer predictions of RAD51B, RAD51C, RAD51D and XRCC2 were docked into the EM density using Dock and Rebuild in Phenix. ATP and Mg2+ were added, and the coordinates were iteratively real space refined using Phenix and manually modified in COOT