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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9MU9
pdb_00009mu9
10.2210/pdb9mu9/pdb
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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
Native purified Nucleosome Elongation Complex 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
36552
Reported Resolution (Å)
7.8
Resolution Method
FSC 0.143 CUT-OFF
Other Details
The Nucleosome EC was refined to an overall resolution of 7.8 A. Then, local refinement was performed with an indvidual focus on the nucleosome and Pol II. This entry represents a composite map of the two locally refined entities.
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 individual models from this study: octameric nucleosome and Pol II. The models were rigid-body fit into the composite structure, connected and fixed in Coot and Phenix.
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
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
