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Structure of Yarrowia lipolytica ORC-Cdc6 bound to 60bp segment of OriA-006 mutant CNNGGNR 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
15.661
f_angle_d
0.5158
f_chiral_restr
0.041
f_bond_d
0.0039
f_plane_restr
0.0038
Sample
ORC-Cdc6 complex of Yarrowia lipolytica bound to a 60bp DNA segment of a mutant of OriA-006 containing the CNNGGNR mutation
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 at 25C and 95% humidity, blotted for 2.7 seconds, and plunged into liquid ethane using a Leica Automatic Plunge Freezer EM GP2.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
51222
Reported Resolution (Å)
2.56
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 YlODC60bpOriA-006-WT structure was docked into the map using ChimeraX and used as a starting point, with the DNA sequence altered at the mutated s ...
The YlODC60bpOriA-006-WT structure was docked into the map using ChimeraX and used as a starting point, with the DNA sequence altered at the mutated sites and manual refinement in Coot used to refine the model.
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)
54.8
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
600
Maximum Defocus (nm)
2000
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
cryoSPARC
4.7.1
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
Patch CTF correction was carried out in cryoSPARC using the default settings, and was optimized during the refinements/reconstruction of the map in cryoSPARC.
2710398
8,428 movies were imported into cryoSPARC and underwent patch motion correction and patch CTF corrections to generate corrected micrographs. Template picking of micrographs commenced using representative 2D class averages of the particles used in the final YlODC60bpOri-A006-WT refinement, resulting in 4,708,382 particles being picked. Micrographs and respective particles were then analyzed using the Micrograph Junk Detector job, and after exposure and particle curation resulted in 2,710,398 particles from 7,330 micrographs. Particles were then extracted with a box size of 432 px and Fourier cropped to 128 px.