EMD-20762

Single-particle
3.6 Å
EMD-20762
3D View Gallery
Deposition: 26/09/2019
Map released: 09/10/2019
Last modified: 20/03/2024
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-20762
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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)
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EMICSS annotations (xml)

Katanin hexamer in the ring conformation in complex with substrate

EMD-20762

Single-particle
3.6 Å
EMD-20762
3D View Gallery
Deposition: 26/09/2019
Map released: 09/10/2019
Last modified: 20/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 1 mg/mL
Buffer
pH: 7.5
Buffer components [5]:
Name Formula Concentration ChEBI
HEPES C8H18N2O4S 20.0 mM
Potassium chloride KCl 300.0 mM
Magnesium dichloride MgCl2 10.0 mM
TCEP C9H15O6P 2.0 mM
ATP C10H16N5O13P3 1.0 mM
Grid
Mesh: 400
Model: C-flat-2/1
Material: GOLD
Pretreatment
Type: PLASMA CLEANING
Time: {'units': 's', 'valueOf_': '15'}
Atmosphere: OTHER
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 90%
Chamber temperature: 279.15 K
Instrument: LEICA EM GP
Details: Load 5 ul sample, wait 10 sec, blot 4.5 sec.
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: 1.0 µm - 2.8000000000000003 µm
Calibrated defocus: 1.0 µm - 2.8000000000000003 µm
Nominal magnification: 130000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Temperature
Minimum: 93.0 K
Maximum: 103.0 K
Specialist optics
Energy filter
Name: GIF Quantum LS
Slit width: 20 eV
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: SUPER-RESOLUTION
Dimensions: 7420 pixel x 7676 pixel
Frames per image: 1-50
Number of grids: 4
Number of real images: 5911
Average exposure time: 10.0 s
Average electron dose per image: 73.0 e/Å2
Image processing [1]
Details: Frames were aligned, dose weighted and summed using MotionCor2
Final reconstruction
Resolution: 3.6 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 108700
Algorithm: FOURIER SPACE
Details:
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION 3.0 -
Startup model [1]
Type: EMDB MAP
EMDB model: EMD-8794
Details:Low-pass filtered to 35 A
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 3.0 -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 3.0 -
Particle selection [1]
Selected Ref. model Method Software Details
1876223 - - - Particles were automatically picked
Final 3D classification
Number of classes: 10
Avg. number of members per classes: 122136.0
Software [1]
Name Version Details
RELION 3.0 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Katanin hexamer in the ring conformation in complex with substrate
⬡ Geometry
X Y Z
Dimensions 224 224 224
Origin 0 0 0
Spacing 224 224 224
Voxel size 1.08 Å 1.08 Å 1.08 Å
Contour list
Primary Level Source
True 5.74 AUTHOR