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- EMDB-9285: MicroED map of cinchonine at 1.0 A resolution -

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Basic information

Entry
Database: EMDB / ID: 9285
TitleMicroED map of cinchonine at 1.0 A resolution
Map data2Fo-Fc map of cinchonine
SampleCinchonine:
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: 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: 0.554685
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.554685
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9285.png

Downloads & links

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Map

Fileemd_9285.map.gz (map file in CCP4 format, 63 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
36 pix
0.31 Å/pix.
= 11.15 Å		36 pix
0.3 Å/pix.
= 10.71 Å		12 pix
0.29 Å/pix.
= 7.06 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

(generated in cubic-lattice coordinate)

Voxel sizeX: 0.2975 Å / Y: 0.29417 Å / Z: 0.30972 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.554685 (by author), 0.554685 (movie #1):
Minimum - Maximum-0.79147947 - 2.417067
Average (Standard dev.)0.000000000807661 (0.36978626)
Details

EMDB XML:

Space Group Number4
Map Geometry
Axis orderYXZ
Dimensions361236
Origin0.00.00.0
Limit35.011.035.0
Spacing362436
CellA: 10.710001 Å / B: 7.0599995 Å / C: 11.15 Å
α: 90.0 deg. / β: 109.665 deg. / γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.29750.294166666666670.30972222222222
M x/y/z362436
origin x/y/z0.0000.0000.000
length x/y/z10.7107.06011.150
α/β/γ90.000109.66590.000
start NX/NY/NZ000
NX/NY/NZ361236
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS123636
D min/max/mean-0.7912.4170.000

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Supplemental data

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Sample components

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Entire Cinchonine

EntireName: Cinchonine / Number of components: 1

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Component #1: cellular-component, Cinchonine

Cellular-componentName: Cinchonine / 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/n / A: 10.71 Å / B: 7.06 Å / C: 11.15 Å / Alpha: 90 deg. / Beta: 109.66 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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