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- EMDB-9292: MicroED structure of thiostrepton at 1.9 A resolution -

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Basic information

Entry
Database: EMDB / ID: 9292
TitleMicroED structure of thiostrepton at 1.9 A resolution
Map data2Fo-Fc map of thiostrepton
SampleThiostrepton:
ligand
Function / homologyThiazolylpeptide-type bacteriocin precursor / defense response to bacterium / extracellular region / Thiostrepton
Function and homology information
SourceStreptomyces azureus (bacteria)
Methodelectron crystallography / cryo EM / 1.91 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
Validation ReportPDB-ID: 6mxf

SummaryFull reportAbout validation report
DateDeposition: Oct 30, 2018 / Header (metadata) release: Nov 21, 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: 0.317655
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.317655
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6mxf
  • Surface level: 0.317655
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6mxf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9292.map.gz (map file in CCP4 format, 372 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
36 pix
0.69 Å/pix.
= 27.534 Å
56 pix
0.6 Å/pix.
= 26.219 Å
46 pix
0.6 Å/pix.
= 26.219 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

(generated in cubic-lattice coordinate)

Voxel sizeX: 0.59589 Å / Y: 0.59589 Å / Z: 0.68834 Å
Density
Contour Level:0.317655 (by author), 0.317655 (movie #1):
Minimum - Maximum-0.51279247 - 1.3747505
Average (Standard dev.)-0.0016757987 (0.21176545)
Details

EMDB XML:

Space Group Number96
Map Geometry
Axis orderYXZ
Dimensions564636
Origin-6.0-10.0-25.0
Limit49.035.010.0
Spacing444440
CellA: 26.219 Å / B: 26.219 Å / C: 27.5336 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.595886363636360.595886363636360.68835
M x/y/z444440
origin x/y/z0.0000.0000.000
length x/y/z26.21926.21927.534
α/β/γ90.00090.00090.000
start NX/NY/NZ-6-10-25
NX/NY/NZ564636
MAP C/R/S213
start NC/NR/NS-10-6-25
NC/NR/NS465636
D min/max/mean-0.5131.375-0.002

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Supplemental data

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Sample components

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Entire Thiostrepton

EntireName: Thiostrepton / Number of components: 3

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Component #1: cellular-component, Thiostrepton

Cellular-componentName: Thiostrepton / Recombinant expression: No
MassTheoretical: 1.619538 kDa
SourceSpecies: Streptomyces azureus (bacteria)

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Component #2: protein, Thiostrepton

ProteinName: Thiostrepton / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.805985 kDa
SourceSpecies: Streptomyces azureus (bacteria)

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Component #3: ligand, water

LigandName: water / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: 3D array / Method: cryo EM
Crystal parametersSpace group: P 43 21 2 / A: 26.219 Å / B: 26.219 Å / C: 27.534 Å / Alpha: 90 deg. / Beta: 90 deg. / Gamma: 90 deg.
Crystal grow detailsPowder
Sample solutionBuffer solution: Powder / pH: 7
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 / Details: FEI Ceta
3D reconstructionResolution: 1.91 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES

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Atomic model buiding

Modeling #1Refinement space: RECIPROCAL
Input PDB model: 1E9W
Chain ID: A

Overall bvalue: 2.6
Output model

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