EMD-10069

Single-particle
3.2 Å
EMD-10069
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Deposition: 13/06/2019
Map released: 18/12/2019
Last modified: 16/10/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-10069
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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)
Map and PDB model 6s01 summary report (pdf.gz) Map and 6s01 FULL report (pdf.gz)
EMICSS annotations (xml)

Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome

EMD-10069

Single-particle
3.2 Å
EMD-10069
3D View Gallery
Deposition: 13/06/2019
Map released: 18/12/2019
Last modified: 16/10/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.2 mg/mL
Details: The complex is purified by gel filtration
Buffer
pH: 7.5
Buffer components [3]:
Name Formula Concentration ChEBI
HEPES C8H18N2O4S 20.0 mM
Sodium chloride NaCl 50.0 mM
Dithiothreitol C4H10O2S2 1.0 mM
Details: Solution were made from stock solution
Grid
Mesh: 200
Model: Quantifoil, UltrAuFoil
Material: GOLD
Pretreatment
Type: GLOW DISCHARGE
Time: 60 s
Atmosphere: AIR
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 277 K
Instrument: FEI VITROBOT MARK IV
Details: Blot for 4 seconds before plunging.
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
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Alignment procedure: COMA FREE
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Average exposure time: 9.0 s
Average electron dose per image: 43.18 e/Å2
Image processing [1]
Final reconstruction
Resolution: 3.2 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 55142
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION 3.0.5 -
Startup model [1]
Type: INSILICO MODEL
Insilico model: CryoSPARC ab-initio reconstruction was use to generate the startup model.
⦨ Initial angle assignment
Type: ANGULAR RECONSTITUTION
⦩ Final angle assignment
Type: ANGULAR RECONSTITUTION
Software [1]
Name Version Details
RELION 3.0.5 -
Particle selection [1]
Selected Ref. model Method Software Details
527640 - - - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Cryo-EM structure of LEDGF bound H3K36me3 modified nucleosome.
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 256 256 256
Dimensions (Å) 268.8 268.8 268.8
Voxel size (Å) 1.05 1.05 1.05
Contour list
Primary Level Source
True 0.05 AUTHOR