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- EMDB-9283: MicroED map of brucine at 0.9 A resolution -

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Basic information

Entry
Database: EMDB / ID: 9283
TitleMicroED map of brucine at 0.9 A resolution
Map data2Fo-Fc map of brucine
SampleBrucine:
Sourcesynthetic construct (others)
Methodelectron crystallography / cryo EM
AuthorsJones CG / Martynowycz MW / Hattne J / Fulton T / Stoltz BM / Rodriguez JA / Nelson HM / Gonen T
CitationJournal: ACS Cent Sci / Year: 2018
Title: The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination.
Authors: Christopher G Jones / Michael W Martynowycz / Johan Hattne / Tyler J Fulton / Brian M Stoltz / Jose A Rodriguez / Hosea M Nelson / Tamir Gonen
DateDeposition: Oct 30, 2018 / Header (metadata) release: Nov 7, 2018 / Map release: Nov 21, 2018 / Last update: Jan 2, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.638175
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.638175
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9283.map.gz (map file in CCP4 format, 218 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
72 pix
0.28 Å/pix.
= 20.01 Å
54 pix
0.28 Å/pix.
= 15.34 Å
14 pix
0.27 Å/pix.
= 7.54 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

(generated in cubic-lattice coordinate)

Voxel sizeX: 0.28407 Å / Y: 0.26929 Å / Z: 0.27792 Å
Density
Contour Level:0.638175 (by author), 0.638175 (movie #1):
Minimum - Maximum-0.84570277 - 3.5762043
Average (Standard dev.)0.000000000199638 (0.42545348)
Details

EMDB XML:

Space Group Number4
Map Geometry
Axis orderYXZ
Dimensions541472
Origin0.00.00.0
Limit53.013.071.0
Spacing542872
CellA: 15.34 Å / B: 7.54 Å / C: 20.01 Å
α: 90.0 deg. / β: 112.495 deg. / γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.284074074074070.269285714285710.27791666666667
M x/y/z542872
origin x/y/z0.0000.0000.000
length x/y/z15.3407.54020.010
α/β/γ90.000112.49590.000
start NX/NY/NZ000
NX/NY/NZ541472
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS145472
D min/max/mean-0.8463.5760.000

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Supplemental data

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Sample components

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Entire Brucine

EntireName: Brucine / Number of components: 1

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Component #1: cellular-component, Brucine

Cellular-componentName: Brucine / Recombinant expression: No
MassTheoretical: 0.362275 kDa
SourceSpecies: synthetic construct (others)

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Experimental details

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Sample preparation

SpecimenSpecimen state: 3D array / Method: cryo EM
Crystal parametersSpace group: P 21 / A: 15.34 Å / B: 7.54 Å / C: 20.01 Å / Alpha: 90 deg. / Beta: 112.49 deg. / Gamma: 90 deg.
Crystal grow detailsPowder
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: Powder / pH: 7
Support filmunspecified
VitrificationCryogen name: NITROGEN / Temperature: 298 K / Humidity: 100 % / Details: Hand-plunged.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 0.09 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: DIFFRACTION
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI CETA (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 28 microns / Details: FEI CetaD

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Image processing

ProcessingMethod: electron crystallography
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES

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Atomic model buiding

Modeling #1Refinement space: RECIPROCAL

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