9MU4 | pdb_00009mu4

Structure of a native Drosophila melanogaster octameric nucleosome

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LZ0
in silico model	AlphaFold	P02299
in silico model	AlphaFold	P84040
in silico model	AlphaFold	P84051
in silico model	AlphaFold	P02283

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	31.791
f_angle_d	0.83
f_chiral_restr	0.047
f_plane_restr	0.007
f_bond_d	0.006

Sample
Natively purified octameric 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	66988
Reported Resolution (Å)	3.29
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The data was processed using cryoSPARC to 3.34 A from 319,428 particles. It was later post-processed using CryoSieve to select the final number of par ...	The data was processed using cryoSPARC to 3.34 A from 319,428 particles. It was later post-processed using CryoSieve to select the final number of particles, yielding 3.29 A.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (3LZ0)
Refinement Space
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value	50
Fitting Procedure
Details	The model was based on PDB: 3LZ0. First, 3LZ0 was rigid-body fit in the cryo-EM Coulomb potential density map using UCSF ChimeraX. Next, AlphaFold2 mo ...	The model was based on PDB: 3LZ0. First, 3LZ0 was rigid-body fit in the cryo-EM Coulomb potential density map using UCSF ChimeraX. Next, AlphaFold2 models for individual Drosophila melanogaster histones were aligned to their 3LZ0 counterparts, and further optimized in the density using rigid-body fit. Then, in Coot, the models were Real-space refined in conjunction with DNA 601 Widom sequence. The DNA sequence was extended, to fit into the density. For the final model optimization, phenix.real_space_refine was used

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
MODEL REFINEMENT	Coot	0.9.8.7
MODEL REFINEMENT	PHENIX	1.21.5207
INITIAL EULER ASSIGNMENT	cryoSPARC	4.3.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.3.1
RECONSTRUCTION	cryoSPARC	4.3.1

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	1848096	Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (1,848,096) is the starting number of particles after initial cleanup and 3D classification of the data.

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.