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Structure of Yarrowia lipolytica ORC-Cdc6 bound to 60bp segment of OriA-006 DNA
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
experimental model
Other
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
16.4328
f_angle_d
0.7522
f_chiral_restr
0.0579
f_bond_d
0.0123
f_plane_restr
0.0059
Sample
ORC-Cdc6 complex of Yarrowia lipolytica bound to a 60bp DNA segment of OriA-006
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
LEICA EM GP
Cryogen Name
ETHANE
Sample Vitrification Details
Sample was applied to a glow-discharged lacey carbon grid and blotted for 3.0 seconds, and plunged into liquid ethane using a Leica Automatic Plunge F ...
Sample was applied to a glow-discharged lacey carbon grid and blotted for 3.0 seconds, and plunged into liquid ethane using a Leica Automatic Plunge Freezer EM GP2.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
125267
Reported Resolution (Å)
2.64
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
The YlODC54bpOriC-061 structure was docked into the map using ChimeraX and used as a starting point, with the DNA sequences substituted and manual ref ...
The YlODC54bpOriC-061 structure was docked into the map using ChimeraX and used as a starting point, with the DNA sequences substituted and manual refinement in Coot used to build the model.
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)
78.8
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
CTF CORRECTION
cryoSPARC
4.7.1
INITIAL EULER ASSIGNMENT
cryoSPARC
4.7.1
FINAL EULER ASSIGNMENT
cryoSPARC
4.7.1
CLASSIFICATION
cryoSPARC
4.7.1
RECONSTRUCTION
cryoSPARC
4.7.1
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 initial screening, and re-corrected in cryoSPARC during the re-picking of particles from micrographs and during the refinements/reconstruction of the map in cryoSPARC
793509
Particle picking used a BoxNet pre-trained neural network implemented in TensorFlow, with a particle diameter of 180 angstrom and a threshold score of 0.4