Home
About
Browse
Covid-19
Organism Classification
Alphafold Collection
Virus Classification
Indian Data
Contact
Search Type
PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
8G57
pdb_00008g57
10.2210/pdb8g57/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
Sirt6 deacetylase bound to a nucleosome assembled with 172-bp 601 Widom DNA
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
71603
Reported Resolution (Å)
3.07
Resolution Method
FSC 0.143 CUT-OFF
Other Details
?
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
?
Overall B Value
79
Fitting Procedure
?
Details
UCSF Chimera was used for manual fitting of the models; It was then used for optimizing the fit by using option Fit in Map. Then Coot was used to analyze the fits, build and adjust the models into the existing densities, and refine parts of the model. Once the model has been built, validated and adjusted, we used phenix.real_space_refine to fix and improve the fit into the densities
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å
2
)
50
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
1200
Maximum Defocus (nm)
2500
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
81000
Calibrated Magnification
81000
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
3.32
IMAGE ACQUISITION
Latitude
?
CTF CORRECTION
cryoSPARC
3.32
MODEL FITTING
UCSF Chimera
1.15
MODEL FITTING
Coot
0.9.8
MODEL REFINEMENT
Coot
0.9.8
MODEL REFINEMENT
PHENIX
1.20
FINAL EULER ASSIGNMENT
cryoSPARC
3.32
CLASSIFICATION
cryoSPARC
3.32
RECONSTRUCTION
cryoSPARC
3.32
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
CTF was estimated using Patch CTF estimation (multi), and was applied during the refinement
