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Search Type
PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9DWM
pdb_00009dwm
10.2210/pdb9dwm/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
Nucleosome containing a 1-nt gap at SHL-5.5
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
7167
Reported Resolution (Å)
4.2
Resolution Method
FSC 0.143 CUT-OFF
Other Details
?
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
?
Refinement Protocol
?
Refinement Target
?
Overall B Value
?
Fitting Procedure
?
Details
?
Data Acquisition
Detector Type
FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å
2
)
50
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
500
Maximum Defocus (nm)
2500
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
?
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
?
Nominal Magnification
?
Calibrated Magnification
?
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
300 kV FEI Titan Krios G3i cryo-TEM equipped with a Falcon 4 direct electron detector and Selectris energy filter
Imaging Experiment
Task
Software Package
Version
CTF CORRECTION
cryoSPARC
v3.3.1
MODEL REFINEMENT
PHENIX
?
INITIAL EULER ASSIGNMENT
cryoSPARC
v3.3.1
FINAL EULER ASSIGNMENT
cryoSPARC
v3.3.1
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
?