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- EMDB-7505: 1.01 A MicroED structure of GSNQNNF at 1.5 e- / A^2 -

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Basic information

Entry
Database: EMDB / ID: 7505
Title1.01 A MicroED structure of GSNQNNF at 1.5 e- / A^2
Map dataMicroED density map
SampleSynthetic proto-filament:
GSNQNNF / (ligand) x 3
Methodelectron crystallography / cryo EM / 1.01 Å resolution
AuthorsHattne J / Shi D
CitationJournal: Structure / Year: 2018
Title: Analysis of Global and Site-Specific Radiation Damage in Cryo-EM.
Authors: Johan Hattne / Dan Shi / Calina Glynn / Chih-Te Zee / Marcus Gallagher-Jones / Michael W Martynowycz / Jose A Rodriguez / Tamir Gonen
Abstract: Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron ...Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron microscopy (cryo-EM). It has been used to solve structures of a diverse set of biomolecules and materials, in some cases to sub-atomic resolution. However, little is known about the damaging effects of the electron beam on samples during such measurements. We assess global and site-specific damage from electron radiation on nanocrystals of proteinase K and of a prion hepta-peptide and find that the dynamics of electron-induced damage follow well-established trends observed in X-ray crystallography. Metal ions are perturbed, disulfide bonds are broken, and acidic side chains are decarboxylated while the diffracted intensities decay exponentially with increasing exposure. A better understanding of radiation damage in MicroED improves our assessment and processing of all types of cryo-EM data.
Validation ReportPDB-ID: 6clm

SummaryFull reportAbout validation report
DateDeposition: Mar 2, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: May 16, 2018 / Last update: May 16, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.34641
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.34641
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6clm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7505.map.gz (map file in CCP4 format, 1714 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
85 pix
0.32 Å/pix.
= 26.918 Å
60 pix
0.3 Å/pix.
= 25.765 Å
84 pix
0.34 Å/pix.
= 20.135 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

(generated in cubic-lattice coordinate)

Voxel sizeX: 0.30312 Å / Y: 0.32045 Å / Z: 0.33558 Å
Density
Contour Level:0.34641 (by author), 0.34641 (movie #1):
Minimum - Maximum-0.6867332 - 1.7302442
Average (Standard dev.)-0.0023458477 (0.23093732)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZXY
Dimensions608485
Origin-36-723
Limit2376107
Spacing858460
CellA: 25.7652 Å / B: 26.9178 Å / C: 20.1348 Å
α: 84.111 deg. / β: 85.159 deg. / γ: 83.018 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.303117647058820.320452380952380.33558333333333
M x/y/z858460
origin x/y/z0.0000.0000.000
length x/y/z25.76526.91820.135
α/β/γ84.11185.15983.018
start NX/NY/NZ-3623-7
NX/NY/NZ608584
MAP C/R/S312
start NC/NR/NS-7-3623
NC/NR/NS846085
D min/max/mean-0.6871.730-0.002

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Supplemental data

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Sample components

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Entire Synthetic proto-filament

EntireName: Synthetic proto-filament / Number of components: 5
MassTheoretical: 0.899141 kDa

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Component #1: protein, Synthetic proto-filament

ProteinName: Synthetic proto-filament / Recombinant expression: No
MassTheoretical: 0.899141 kDa

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Component #2: protein, GSNQNNF

ProteinName: GSNQNNF / Recombinant expression: No
MassTheoretical: 0.779756 kDa

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Component #3: ligand, ACETATE ION

LigandName: ACETATE IONAcetate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.904405 MDa

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Component #4: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #5: ligand, water

LigandName: water / Number of Copies: 3 / 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: P1 / A: 4.85 Å / B: 14.1 Å / C: 17.45 Å / Alpha: 84.111 deg. / Beta: 85.159 deg. / Gamma: 83.018 deg.
Sample solutionSpecimen conc.: 10 mg/ml / pH: 6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 3 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 0.00357 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: DIFFRACTION
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1012 / Sampling size: 31.2 microns

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Image processing

ProcessingMethod: electron crystallography
3D reconstructionResolution: 1.01 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES

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Atomic model buiding

Output model

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