EMDB-8594: Automated tomogram annotation of PC12 cell

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ID or keywords:

Entry	Database: EMDB / ID: 8594
Title	Automated tomogram annotation of PC12 cell
Sample	PC12 cell
Source	Rattus / mammal / image: Rattus norvegicus
Map data	Automated tomogram annotation of PC12 cell
Method	electron tomography
Authors	Chen M / Dai W / Schmid MF / Chiu W / Ludtke SJ
Citation	To Be Published To Be Published Search PubMed Convolutional Neural Networks for Automated Annotation of Cellular Cryo-Electron Tomograms Chen M / Dai W / Sun SY / Jonasch D / He CY / Schmid MF / Chiu W / Ludtke SJ
Date	Deposition: Feb 3, 2017 / Header (metadata) release: Mar 1, 2017 / Map release: Mar 1, 2017 / Last update: Feb 3, 2017

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Supplemental images

emd_8594.png

Map data	emd_8594.map.gz (206.9 MB)
Header (meta data in XML format)	emd-8594-v19.xml (4.7 KB) / emd-8594-v20.xml (15 KB) / emd-8594.xml (4.7 KB)
Images	emd_8594.png (346.1 KB)
Others	emd_8594_additional_1.map.gz (124.8 MB) / emd_8594_additional_2.map.gz (137.4 MB) / emd_8594_additional_3.map.gz (98.5 MB) / emd_8594_additional_4.map.gz (113.7 MB)
FTP directory	ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8594

Legacy pages	EM Navigator legacy / Yorodumi legacy
EMDB pages	PDBe / RCSB PDB

Related structure data	C8589 C8590 C8591 C8592 C8593 C: citing same article
Similar-shape strucutres	Search similar-shape structures by Omokage search (details)

File

emd_8594.map.gz (map file in CCP4 format, 234091 KB)

Projections & slices

Size
Brightness
Contrast
Others	InvertY flip

Axes	Z (Sec.)	Y (Row.)	X (Col.)
	81 pix 28.6 Å/pix. = 2316.6 Å	850 pix 28.6 Å/pix. = 24310. Å	850 pix 28.6 Å/pix. = 24310. Å
Surface
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Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider package.

Voxel size

X=Y=Z: 28.6 Å

Density

Histogram

Histogram (log scale)

Contour Level:	0.1 (by emdb)
Minimum - Maximum	-14.392706 - 25.645239
Average (Standard dev.)	-1.81239E-10 (1)

Details

EMDB XML:

Space Group Number

1

Map Geometry

Axis order	X	Y	Z
Dimensions	850	850	81
Origin	-425	-425	-40
Limit	424	424	40
Spacing	850	850	81

Cell

A: 24310 Å / B: 24310 Å / C: 2316.6 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

mode	Image stored as Reals
A/pix X/Y/Z	28.6	28.6	28.6
M x/y/z	850	850	81
origin x/y/z	0.000	0.000	0.000
length x/y/z	24310.000	24310.000	2316.600
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S	1	2	3
start NC/NR/NS	-425	-425	-40
NC/NR/NS	850	850	81
D min/max/mean	-14.393	25.645	-0.000

Entire	Name: PC12 cell / Number of components: 1

Cellular-component	Name: PC12 cell / Recombinant expression: No
Source	Species: Rattus / mammal / image: Rattus norvegicus

Specimen state	cell
Sample solution	pH: 7
Vitrification	Cryogen name: ETHANE

Imaging	Microscope: JEOL 2100
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å² / Illumination mode: FLOOD BEAM
Lens	Imaging mode: BRIGHT FIELD
Specimen Holder	Model: OTHER
Camera	Detector: GATAN ULTRASCAN 4000 (4k x 4k)

Processing	Method: electron tomography / Number of sections: 30
3D reconstruction	Algorithm: BACK PROJECTION

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