Electron Microscopy Data Bank

EMD-2301

Single-particle
26.5 Å

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Deposition: 25/01/2013
Map released: 13/02/2013
Last modified: 03/04/2013

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EMD-2301

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Negative stain EM structure of TcdA1 in pore state

EMD-2301

Single-particle
26.5 Å
EMD-2301

3D View Gallery

Deposition: 25/01/2013
Map released: 13/02/2013
Last modified: 03/04/2013

Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

Method: Single-particle
Aggregation State: Particle

Summary:

Specimen preparation
Microscopy
Image processing
Map

Specimen preparation [1]

Concentration: 0.02 mg/mL

Buffer

pH: 11.0
Details: 50 mM CAPS, mM NaCl, 0.05% Tween-20, 5% glycerol

Staining

Type: NEGATIVE
Details: Grids with adsorbed Protein floated on 0.07% Uranyl Formate for 45 sec.

Grid

Details: Glow discharged 400 mesh copper grids with thin carbon support

Vitrification

Cryogen name: NONE
Instrument: OTHER

Microscopy [1]

Microscope: JEOL 1400
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: LAB6
Acceleration voltage: 120 kV
Nominal CS: 3.4 mm
Nominal defocus: 0.0012 µm - 0.002 µm
Nominal magnification: 50000.0
Calibrated magnification: 67210.0
Specimen holder model: JEOL

Image Recording [1]

Detector category: CCD
Detector model: TVIPS TEMCAM-F416 (4k x 4k)
Number of real images: 80

Image processing [1]

Final reconstruction

Resolution: 26.5 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 1936
Algorithm: OTHER

Applied Symmetry

Point group: C5

Software [1]

Name	Version	Details
Sparx	-	-

Map

Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Negative stain reconstruction of TcdA1 in pore state
Details: ::::EMDATABANK.org::::EMD-2301::::

Geometry

	X	Y	Z
Dimensions	112	112	112
Origin	0	0	0
Spacing	112	112	112
Voxel size	4.64 Å	4.64 Å	4.64 Å

Contour list

Primary	Level	Source
True	0.038	AUTHOR