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 6R0C | pdb_00006r0c

Human-D02 Nucleosome Core Particle with biotin-streptavidin label


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UTB 
Sample
Human-D02 Nucleosome Core Particle with biotin-streptavidin label
Sample Components
Histones
DNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles62196
Reported Resolution (Å)4.2
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (3UTB)
Refinement SpaceREAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
DetailsThe initial model was placed in the density using Chimera. Manual building was performed in Coot and final refinement was carried out using phenix.rea ...The initial model was placed in the density using Chimera. Manual building was performed in Coot and final refinement was carried out using phenix.real_space_refine. Additional restraints describing protein secondary structure, DNA base pairing and stacking were used in Phenix.
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)28.3
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1.5
Maximum Defocus (nm)3.5
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification75000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION2.1
IMAGE ACQUISITIONEPU
CTF CORRECTIONGctf1.08
MODEL FITTINGCoot
INITIAL EULER ASSIGNMENTRELION2.1
FINAL EULER ASSIGNMENTRELION2.1
CLASSIFICATIONRELION2.1
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION3712obvious micrographs with cubic ice were discarded