EMD-6740

Single-particle
11.5 Å
EMD-6740
3D View Gallery
Deposition: 22/05/2017
Map released: 31/01/2018
Last modified: 05/08/2020
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-6740
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3D volume (map.gz) Experimental metadata (xml) Experimental Metadata (cif.gz)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
EMICSS annotations (xml)

Human HP1alpha-dinucleosome H3K9Me3 class C

EMD-6740

Single-particle
11.5 Å
EMD-6740
3D View Gallery
Deposition: 22/05/2017
Map released: 31/01/2018
Last modified: 05/08/2020
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: .8 mg/mL
Details: Sample was monodisperse
Buffer
pH: 7.5
Buffer components [2]:
Name Formula Concentration ChEBI
Tris-HCl (HOCH2)3CNH2 20.0 mM
DTT Dithiothreitol 1.0 mM
Grid
Mesh: 200
Model: Quantifoil R1.2/1.3
Material: COPPER
Details: Gatan Solarus
Pretreatment
Type: PLASMA CLEANING
Atmosphere: OTHER
Pressure: 9.33 kPa
Support Film [1]
Material Topology Thickness
CARBON HOLEY 100.0 nm
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 289 K
Instrument: FEI VITROBOT MARK IV
Details: 3 second blot, 2.5uL.
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 50.0 µm
Nominal CS: 2.62 mm
Nominal magnification: 105000.0
Calibrated magnification: 35971.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE ( Residual tilt: 0.1 mrad)
Details: Nanoprobe, parallel beam illumination
Temperature
Minimum: 77.0 K
Maximum: 100.0 K
Specialist optics
Phase plate: VOLTA PHASE PLATE
Energy filter
Name: Gatan Quantum 968
Lower energy threshold: -10 eV
Upper energy threshold: 10 eV
Image Recording [1]
Detector model: GATAN K2 QUANTUM (4k x 4k)
Detector mode: COUNTING
Dimensions: 3838 pixel x 3710 pixel
Sampling interval: 5.0 µm
Frames per image: 1-40
Number of grids: 2
Number of real images: 2329
Average exposure time: 5.0 s
Average electron dose per image: 38.0 e/Å2
Details: Images were collected with a volta phase plate (VPP) in-focus
Image processing [1]
Details: Frame alignment and integration with motioncor2 incl. dose weighting
Final reconstruction
Resolution: 11.5 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 21344
Algorithm: FOURIER SPACE
Details:
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION 2.1 -
Startup model [1]
Type: OTHER
Details:Cylinder generated in SPIDER
⦨ Initial angle assignment
Type: PROJECTION MATCHING
Software [1]
Name Version Details
RELION 2.0 -
⦩ Final angle assignment
Type: PROJECTION MATCHING
Software [1]
Name Version Details
RELION 2.1 -
Particle selection [1]
Selected Ref. model Method Software Details
409948 - - - -
Final 3D classification
Number of classes: 6
Avg. number of members per classes: 22000.0
Software [1]
Name Version Details
RELION 2.1 -
CTF correction
Details: In-focus VPP data
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 256 256 256
Dimensions (Å) 355.84 355.84 355.84
Voxel size (Å) 1.39 1.39 1.39
Contour list
Primary Level Source
True 3.11 AUTHOR