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- EMDB-17992: Structure of K27A mutant E.coli DPS -

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Basic information

Entry
Database: EMDB / ID: EMD-17992
TitleStructure of K27A mutant E.coli DPS
Map dataStructure of K27A mutant E.coli DPS determined by movement-free cryoEM.
Sample
  • Complex: DNA protection during starvation protein (DPS)
    • Protein or peptide: DNA protection during starvation protein (DPS)
Keywordsferritin / DNA / METAL BINDING PROTEIN
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.8 Å
AuthorsDickerson JL / Russo CJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Ultramicroscopy / Year: 2024
Title: Accurate magnification determination for cryoEM using gold.
Authors: Joshua L Dickerson / Erin Leahy / Mathew J Peet / Katerina Naydenova / Christopher J Russo /
Abstract: Determining the correct magnified pixel size of single-particle cryoEM micrographs is necessary to maximize resolution and enable accurate model building. Here we describe a simple and rapid ...Determining the correct magnified pixel size of single-particle cryoEM micrographs is necessary to maximize resolution and enable accurate model building. Here we describe a simple and rapid procedure for determining the absolute magnification in an electron cryomicroscope to a precision of <0.5%. We show how to use the atomic lattice spacings of crystals of thin and readily available test specimens, such as gold, as an absolute reference to determine magnification for both room temperature and cryogenic imaging. We compare this method to other commonly used methods, and show that it provides comparable accuracy in spite of its simplicity. This magnification calibration method provides a definitive reference quantity for data analysis and processing, simplifies the combination of multiple datasets from different microscopes and detectors, and improves the accuracy with which the contrast transfer function of the microscope can be determined. We also provide an open source program, magCalEM, which can be used to accurately estimate the magnified pixel size of a cryoEM dataset ex post facto.
History
DepositionJul 20, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17992.png

Downloads & links

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Map

FileDownload / File: emd_17992.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of K27A mutant E.coli DPS determined by movement-free cryoEM.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 320 pix.
= 206.72 Å		0.65 Å/pix.
x 320 pix.
= 206.72 Å		0.65 Å/pix.
x 320 pix.
= 206.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.646 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0275
Minimum - Maximum-0.048345856 - 0.13302141
Average (Standard dev.)0.00012093023 (±0.003445426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 206.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17992_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 1

Fileemd_17992_half_map_1.map
AnnotationUnfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 2

Fileemd_17992_half_map_2.map
AnnotationUnfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DNA protection during starvation protein (DPS)

EntireName: DNA protection during starvation protein (DPS)
Components
  • Complex: DNA protection during starvation protein (DPS)
    • Protein or peptide: DNA protection during starvation protein (DPS)

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Supramolecule #1: DNA protection during starvation protein (DPS)

SupramoleculeName: DNA protection during starvation protein (DPS) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 224 KDa

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Macromolecule #1: DNA protection during starvation protein (DPS)

MacromoleculeName: DNA protection during starvation protein (DPS) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSTAKLVKSK ATNLLYTRND VSDSEKAATV ELLNRQVIQF IDLSLITKQA HWNMRGANFI AVHEMLDGFR TALIDHLDTM AERAVQLGG VALGTTQVIN SKTPLKSYPL DIHNVQDHLK ELADRYAIVA NDVRKAIGEA KDDDTADILT AASRDLDKFL W FIESNIE

UniProtKB: UNIPROTKB: POABT2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.7
GridMaterial: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 30 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

11210

Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 1.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 234690
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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