Home
About
Browse
Covid-19
Organism Classification
Alphafold Collection
Indian Data
Contact
Search Type
PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9MU4
pdb_00009mu4
10.2210/pdb9mu4/pdb
Download file
FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Natively purified octameric nucleosome from Drosophila melanogaster
Specimen Preperation
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 particles, yielding 3.29 A.
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
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 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
Date of Experiment
?
Temprature (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
?
Imaging Experiment
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
