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- EMDB-1856: Automatic Recovery of Missing Amplitudes and Phases in Tilt-Limit... -

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Basic information

Entry
Database: EMDB / ID: EMD-1856
TitleAutomatic Recovery of Missing Amplitudes and Phases in Tilt-Limited Electron Crystallography of 2D Crystals
Map dataCrystal unit cell of 3D-PCO reconstructed bacteriorhodopsin. Generated from original MTZ limited from 15.0 A to 2.5 A.
Sample
  • Sample: Bacteriorhodopsin
  • Protein or peptide: Bacteriorhodopsin
KeywordsCrystallography / Signal Recovery / Iterative Methods / Oversampling / Tilt-Limited / Electron Microscopy
Biological speciesHalobacterium salinarum (Halophile)
Methodelectron crystallography / cryo EM
AuthorsGipson B / Masiel DJ / Browning ND / Spence J / Mitsuoka K / Stahlberg H
CitationJournal: Phys Rev E Stat Nonlin Soft Matter Phys / Year: 2011
Title: Automatic recovery of missing amplitudes and phases in tilt-limited electron crystallography of two-dimensional crystals.
Authors: Bryant R Gipson / Daniel J Masiel / Nigel D Browning / John Spence / Kaoru Mitsuoka / Henning Stahlberg /
Abstract: Electron crystallography of 2D protein crystals provides a powerful tool for the determination of membrane protein structure. In this method, data is acquired in the Fourier domain as randomly ...Electron crystallography of 2D protein crystals provides a powerful tool for the determination of membrane protein structure. In this method, data is acquired in the Fourier domain as randomly sampled, uncoupled, amplitudes and phases. Due to physical constraints on specimen tilting, those Fourier data show a vast un-sampled "missing cone" of information, producing resolution loss in the direction perpendicular to the membrane plane. Based on the flexible language of projection onto sets, we provide a full solution for these problems with a projective constraint optimization algorithm that, for sufficiently oversampled data, produces complete recovery of unmeasured data in the missing cone. We apply this method to an experimental data set of Bacteriorhodopsin and show that, in addition to producing superior results compared to traditional reconstruction methods, full, reproducible, recovery of the missing cone from noisy data is possible. Finally, we present an automatic implementation of the refinement routine as open source, freely distributed, software that will be included in our 2dx software package.
History
DepositionJan 7, 2011-
Header (metadata) releaseOct 3, 2012-
Map releaseOct 3, 2012-
UpdateNov 7, 2012-
Current statusNov 7, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1856.png

Downloads & links

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Map

FileDownload / File: emd_1856.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCrystal unit cell of 3D-PCO reconstructed bacteriorhodopsin. Generated from original MTZ limited from 15.0 A to 2.5 A.
Voxel sizeX: 0.82171 Å / Y: 0.82171 Å / Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.04189055 - 0.05812847
Average (Standard dev.)-0.00000138 (±0.0082718)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA: 82.171 Å / B: 82.171 Å / C: 100.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.821710.821711
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z82.17182.171100.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-24-70
NX/NY/NZ6149141
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0420.058-0.000

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Supplemental data

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Sample components

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Entire : Bacteriorhodopsin

EntireName: Bacteriorhodopsin
Components
  • Sample: Bacteriorhodopsin
  • Protein or peptide: Bacteriorhodopsin

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Supramolecule #1000: Bacteriorhodopsin

SupramoleculeName: Bacteriorhodopsin / type: sample / ID: 1000 / Details: Exactly as per PDB entry 1at9 (same dataset) / Number unique components: 1

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Macromolecule #1: Bacteriorhodopsin

MacromoleculeName: Bacteriorhodopsin / type: protein_or_peptide / ID: 1 / Name.synonym: BR / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Halobacterium salinarum (Halophile)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

VitrificationCryogen name: NITROGEN / Chamber temperature: 4.2 K / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL KYOTO-3000SFF
DetailsThe full details of the original dataset can be found from PDB entry 1at9
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Sample stageSpecimen holder: As per 1at9 / Specimen holder model: JEOL

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Image processing

Final reconstructionAlgorithm: OTHER / Software - Name: 2dx (PCO Module)
Details: 3D-PCO reconstructed maps, generated from phase-flipped raw 2D kimura, 97 crystallographic dataset.
Crystal parametersPlane group: P 3
CTF correctionDetails: Phase flipping and Electron Diffraction

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