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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9BYQ
pdb_00009byq
10.2210/pdb9byq/pdb
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FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Asymmetric subunit of the BALF2 ssDNA-annealing filament
Specimen Preperation
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 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
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 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
Date of Experiment
?
Temprature (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
Imaging Experiment
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
?
