EMD-4318

Single-particle
4.5 Å
EMD-4318
3D View Gallery
Deposition: 25/02/2018
Map released: 08/08/2018
Last modified: 17/10/2018
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-4318
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3D volume (map.gz) Experimental metadata (xml)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 6ftx summary report (pdf.gz) Map and 6ftx FULL report (pdf.gz)
EMICSS annotations (xml)

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

EMD-4318

Single-particle
4.5 Å
EMD-4318
3D View Gallery
Deposition: 25/02/2018
Map released: 08/08/2018
Last modified: 17/10/2018
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 1 mg/mL
Details: Sample was gel filtration purified and it is monodisperse
Buffer
pH: 7.5
Buffer components [2]:
Name Formula Concentration ChEBI
Hepes - 20.0 mM -
NaCl - 100.0 mM -
Grid
Mesh: 400
Model: C-flat-1.2/1.3 4C
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere: OTHER
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 277 K
Instrument: FEI VITROBOT MARK III
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: 70.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 1.5 µm - 4.0 µm
Calibrated defocus: 1.5 µm - 4.0 µm
Nominal magnification: 35714.0
Calibrated magnification: 35714.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: BASIC
Temperature
Minimum: 170.0 K
Maximum: 170.0 K
Specialist optics
Energy filter
Name: GIF Quantum LS
Image Recording [1]
Detector model: GATAN K2 QUANTUM (4k x 4k)
Detector mode: COUNTING
Dimensions: 3870 pixel x 3870 pixel
Sampling interval: 5.0 µm
Frames per image: 5-28
Number of grids: 1
Number of real images: 1300
Average exposure time: 0.32 s
Average electron dose per image: 1.25 e/Å2
Image processing [1]
Final reconstruction
Resolution: 4.5 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 135000
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION - -
Startup model [1]
Type: EMDB MAP
EMDB model: EMD-3502
⦨ Initial angle assignment
Type: ANGULAR RECONSTITUTION
Software [1]
Name Version Details
RELION - -
⦩ Final angle assignment
Type: ANGULAR RECONSTITUTION
Software [1]
Name Version Details
RELION - -
Particle selection [1]
Selected Ref. model Method Software Details
860000 - - - -
Final 3D classification
Software [1]
Name Version Details
RELION - -
CTF correction
Software [1]
Name Version Details
Gctf - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: CryoEM reconstruction for a S.cerevisiae chromatin remodeller bound to 601 nucleosome.
⬡ Geometry
X Y Z
Dimensions 240 240 240
Origin 0 0 0
Spacing 240 240 240
Voxel size 1.4 Å 1.4 Å 1.4 Å
Contour list
Primary Level Source
True 0.011 AUTHOR