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 8G57 | pdb_00008g57

Structure of nucleosome-bound Sirtuin 6 deacetylase


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LZ0 
experimental modelPDB 3PKI 
experimental modelPDB 7CL0 
Sample
Sirt6 deacetylase bound to a nucleosome assembled with 172-bp 601 Widom DNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles71603
Reported Resolution (Å)3.07
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (3LZ0, 3PKI, 7CL0)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value79
Fitting Procedure
DetailsUCSF 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 anal ...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 TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1200
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification81000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.32
IMAGE ACQUISITIONLatitude
CTF CORRECTIONcryoSPARC3.32
MODEL FITTINGUCSF Chimera1.15
MODEL FITTINGCoot0.9.8
MODEL REFINEMENTCoot0.9.8
MODEL REFINEMENTPHENIX1.20
FINAL EULER ASSIGNMENTcryoSPARC3.32
CLASSIFICATIONcryoSPARC3.32
RECONSTRUCTIONcryoSPARC3.32
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTF was estimated using Patch CTF estimation (multi), and was applied during the refinement12821862Particles were selected using Blob Picker