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Structure of Yarrowia lipolytica ORC-Cdc6 bound to 54bp segment of OriC-061 DNA
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
in silico model
Other
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
15.6348
f_angle_d
0.4694
f_chiral_restr
0.0388
f_plane_restr
0.0038
f_bond_d
0.003
Sample
ORC-Cdc6 complex of Yarrowia lipolytica bound to a 54bp DNA segment of OriC-061
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
LEICA EM GP
Cryogen Name
ETHANE
Sample Vitrification Details
Sample was applied to a non-glow discharged Quantifoil R 1.2/1.3 300 mesh copper grid (previously washed with ethyl acetate), incubated for 10 seconds ...
Sample was applied to a non-glow discharged Quantifoil R 1.2/1.3 300 mesh copper grid (previously washed with ethyl acetate), incubated for 10 seconds, blotted for 2.9 seconds, and plunged into liquid ethane using a Leica Automatic Plunge Freezer EM GP2.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
51599
Reported Resolution (Å)
2.73
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Non-uniform refinement was used for the final reconstruction.
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
AlphaFold 2 models for each subunit were docked into the density individually using the "fit to map" functionality in ChimeraX, then refined using Coo ...
AlphaFold 2 models for each subunit were docked into the density individually using the "fit to map" functionality in ChimeraX, then refined using Coot. The density for the DNA was sharp enough to allow us to discern purines and pyrimidines, allowing us to produce a generic DNA-B form model of the respective DNA sequence and manually rebuild it in Coot. PHENIX Real Space Refine functionality was used to further process and finalize the structure.
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)
43.2
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
600
Maximum Defocus (nm)
2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
105000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
Warp
MODEL REFINEMENT
PHENIX
2.0_5885
RECONSTRUCTION
cryoSPARC
4.7
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
CTF correction was done first in WARP during exposure/micrograph pre-processing, and re-corrected during the final refinements/reconstruction of the map in cryoSPARC
3805196
Particle picking used a BoxNet pre-trained neural network implemented in TensorFlow, with a particle diameter of 180 angstrom and a threshold score of 0.5