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Structure of a native Drosophila melanogaster hexameric nucleosome
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
32.647
f_angle_d
0.715
f_chiral_restr
0.04
f_plane_restr
0.005
f_bond_d
0.004
Sample
Natively purified hexameric nucleosome from Drosophila melanogaster
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
38738
Reported Resolution (Å)
6.3
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
The model was based on octameric nucleosome from this study. Coot and Phenix were used to adjust the existing model to the hexameric nucleosome densit ...
The model was based on octameric nucleosome from this study. Coot and Phenix were used to adjust the existing model to the hexameric nucleosome density.
Data Acquisition
Detector Type
FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)
50.65
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS TALOS
Minimum Defocus (nm)
1000
Maximum Defocus (nm)
2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.3.1
IMAGE ACQUISITION
EPU
3.4
CTF CORRECTION
cryoSPARC
4.3.1
MODEL FITTING
UCSF ChimeraX
1.8
INITIAL EULER ASSIGNMENT
cryoSPARC
4.3.1
FINAL EULER ASSIGNMENT
cryoSPARC
4.3.1
RECONSTRUCTION
cryoSPARC
4.3.1
MODEL REFINEMENT
Coot
0.9.8.7
MODEL REFINEMENT
PHENIX
1.21.5207
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
'Patch CTF Estimation' in cryoSPARC
231425
Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (231,425) is the starting number of particles after initial cleanup and 3D classification of the data.