6ZHY

Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class.


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LZ0 
experimental modelPDB 1ZLA 
Sample
A hexasome (nucleosome lacking one of the two H2A-H2B dimers) with its acidic patch bound by the ALC1 linker regulatory region.
Sample Components
Histones
DNA
Chromodomain-helicase-DNA-binding protein 1-like
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlot time 2.5 s, blot force 0. Two sample applications and blots were performed before vitrification.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles414641
Reported Resolution (Å)3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (3LZ0, 3LZ0, 3LZ0, 3LZ0, 3LZ0, 3LZ0, 3LZ0, 3LZ0, 1ZLA)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetReal-space CC between model and map
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50.4
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONEPU2.6.1
CTF CORRECTIONGctf1.18b2
MODEL FITTINGUCSF Chimera0.93
INITIAL EULER ASSIGNMENTRELION3.1
FINAL EULER ASSIGNMENTRELION3.1
CLASSIFICATIONRELION3.1
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTISOLDE1.0b5
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION2968853