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 7UV9 | pdb_00007uv9

KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7JO9 
Sample
KDM2A-nucleosome complex stabilized by H3K36C-UNC8015 covalent conjugate
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles55125
Reported Resolution (Å)3.2
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (7JO9)
Refinement SpaceREAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)45
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TALOS ARCTICA
Minimum Defocus (nm)500
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification45000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.1
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONCTFFIND4.1
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTRELION3.1
FINAL EULER ASSIGNMENTRELION3.1
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.19
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION2171614