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- EMDB-9289: MicroED map of (+)-limaspermidine at 0.77 A resolution -

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Basic information

Entry
Database: EMDB / ID: 9289
TitleMicroED map of (+)-limaspermidine at 0.77 A resolution
Map data2Fo-Fc map of limasperimidine
Sample(+)-limaspermidine:
Sourcesynthetic construct (others)
Methodelectron crystallography / cryo EM / 0.77 Å resolution
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: Jones CG / Martynowycz MW / Hattne J / Fulton T / Stoltz BM / Rodriguez JA / Nelson HM / Gonen T
DateDeposition: Oct 30, 2018 / Header (metadata) release: Nov 7, 2018 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.64422
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.64422
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9289.map.gz (map file in CCP4 format, 116 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
15 pix
0.25 Å/pix.
= 13.88 Å
32 pix
0.24 Å/pix.
= 7.62 Å
60 pix
0.25 Å/pix.
= 15.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

(generated in cubic-lattice coordinate)

Voxel sizeX: 0.23813 Å / Y: 0.24786 Å / Z: 0.25333 Å
Density
Contour Level:0.64422 (by author), 0.64422 (movie #1):
Minimum - Maximum-0.7562673 - 3.6278906
Average (Standard dev.)0.0012259927 (0.429481)
Details

EMDB XML:

Space Group Number19
Map Geometry
Axis orderZXY
Dimensions326015
Origin0.00.00.0
Limit31.059.014.0
Spacing325660
CellA: 7.62 Å / B: 13.88 Å / C: 15.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.2381250.247857142857140.25333333333333
M x/y/z325660
origin x/y/z0.0000.0000.000
length x/y/z7.62013.88015.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ321560
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS603215
D min/max/mean-0.7563.6280.001

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Supplemental data

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Sample components

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Entire (+)-limaspermidine

EntireName: (+)-limaspermidine / Number of components: 1

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Component #1: cellular-component, (+)-limaspermidine

Cellular-componentName: (+)-limaspermidine / Recombinant expression: No
MassTheoretical: 0.272217 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 21 21 / A: 7.62 Å / B: 13.88 Å / C: 15.2 Å / Alpha: 90 deg. / Beta: 90 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: 0.77 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES

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Atomic model buiding

Modeling #1Refinement space: RECIPROCAL

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