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- EMDB-40602: cryoEM map for design HE0537, a D4 symmetric homo-oligomer design... -

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Basic information

Entry
Database: EMDB / ID: EMD-40602
TitlecryoEM map for design HE0537, a D4 symmetric homo-oligomer designed with RFdiffusion.
Map dataRefined cryoEM map for design HE0537
Sample
  • Complex: HE0537
KeywordsDe novo / computationally designed / Dihedral / diffusion model / RFdiffusion / BIOSYNTHETIC PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.06 Å
AuthorsCourbet A / Baker D / Watson J / Juergens D / Eisenach E
Funding support United States, 3 items
OrganizationGrant numberCountry
Other private United States
Other governmentS10OD032290 United States
Other governmentP30 CA015704-40 United States
CitationJournal: To Be Published
Title: Broadly applicable protein design with RoseTTAFold Diffusion
Authors: Juergens D / Watson J / Eisenach HE / Courbet A
History
DepositionApr 26, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40602.png

Downloads & links

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Map

FileDownload / File: emd_40602.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined cryoEM map for design HE0537
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 256 pix.
= 226.048 Å		0.88 Å/pix.
x 256 pix.
= 226.048 Å		0.88 Å/pix.
x 256 pix.
= 226.048 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.883 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-0.002603008 - 1.8033969
Average (Standard dev.)0.002212746 (±0.034970436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 226.048 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40602_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of cryoEM map for design HE0537

Fileemd_40602_half_map_1.map
AnnotationHalf map A of cryoEM map for design HE0537
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of cryoEM map for design HE0537

Fileemd_40602_half_map_2.map
AnnotationHalf map B of cryoEM map for design HE0537
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HE0537

EntireName: HE0537
Components
  • Complex: HE0537

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Supramolecule #1: HE0537

SupramoleculeName: HE0537 / type: complex / ID: 1 / Parent: 0
Details: De novo D4 symmetric homooligomer designed with RFdiffusion
Source (natural)Organism: synthetic construct (others)

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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

Concentration10 mg/mL
BufferpH: 8.4
Component:
ConcentrationFormulaName
100.0 mMNaClSodium Chloride
25.0 mMTrisTris
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1116 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 6.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.1.2) / Number images used: 36827
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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