9BYQ | pdb_00009byq

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.

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	65

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Preliminary Grid screening was performed manually

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4
IMAGE ACQUISITION	EPU	3
IMAGE ACQUISITION	cryoSPARC	4
CTF CORRECTION	cryoSPARC	4
MODEL FITTING	ISOLDE	1.3
MODEL REFINEMENT	PHENIX	1.2.1
INITIAL EULER ASSIGNMENT	cryoSPARC	4
FINAL EULER ASSIGNMENT	cryoSPARC	4
CLASSIFICATION	cryoSPARC	4
RECONSTRUCTION	cryoSPARC	4

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		3311483

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.