EMD-5588

Single-particle
15.0 Å
EMD-5588
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Deposition: 26/02/2013
Map released: 17/04/2013
Last modified: 15/05/2013
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EMD-5588
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Electron cryo-microscopy of the yeast Mediator Cdk8 kinase module

EMD-5588

Single-particle
15.0 Å
EMD-5588
3D View Gallery
Deposition: 26/02/2013
Map released: 17/04/2013
Last modified: 15/05/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.020 mg/mL
Buffer
pH: 7.6
Details: 20mM HEPES, 200mM potassium acetate, 5mM beta-mercaptoethanol
Grid
Details: 300 mesh Cu/Rh grids with continuous carbon, glow discharged in amylamine atmosphere
Vitrification
Cryogen name: ETHANE
Chamber humidity: 95%
Chamber temperature: 77 K
Instrument: HOMEMADE PLUNGER
Microscopy [1]
Microscope: FEI TECNAI F20
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 120 kV
Nominal CS: 1.2 mm
Nominal defocus: 1.5 µm - 4.0 µm
Nominal magnification: 60000.0
Calibrated magnification: 60400.0
Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 125,000 times magnification using a CCD camera, Electron beam tilt params: )
Temperature
Minimum: 80 K
Average: 105 K
Maximum: 110 K
Image Recording [1]
Detector category: FILM
Detector model: KODAK SO-163 FILM
Scanner: NIKON SUPER COOLSCAN 9000
Sampling interval: 6.35 µm
Number of real images: 154
Average electron dose per image: 15 e/Å2
Bits per pixel: 16.0
Image processing [1]
Final reconstruction
Resolution: 15.0 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 70000
Algorithm: OTHER
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
SPARX, SPIDER - -
CTF correction
Details:Each particle
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Map of the CDK8 kinase module including Med12, Med13, Cdk8, and CycC
Details: ::::EMDATABANK.org::::EMD-5588::::
⬡ Geometry
X Y Z
Dimensions 144 144 144
Origin 0 0 0
Spacing 144 144 144
Voxel size 2.1 Å 2.1 Å 2.1 Å
Contour list
Primary Level Source
True 0.00105 EMDB