Ab-initio phasing using nanocrystal shape transforms with incomplete unit cells

Haiguang Liu, Nadia Zatsepin, John Spence

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

X-ray free electron lasers are used in measuring diffraction patterns from nanocrystals in the 'diffract-before-destroy' mode by outrunning radiation damage. The finite-sized nanocrystals provide an opportunity to recover intensity between Bragg spots by removing the modulating function that depends on crystal shape, i.e. the transform of the crystal shape. This shape-transform dividing-out scheme for solving the phase problem has been tested using simulated examples with cubic crystals. It provides a phasing method which does not require atomic resolution data, chemical modification to the sample, or modelling based on the protein databases. It is common to find multiple structural units (e.g. molecules, in symmetry-related positions) within a single unit cell, therefore incomplete unit cells (e.g. one additional molecule) can be observed at surface layers of crystals. In this work, the effects of such incomplete unit cells on the 'dividing-out' phasing algorithm are investigated using 2D crystals within the projection approximation. It is found that the incomplete unit cells do not hinder the recovery of the scattering pattern from a single unit cell (after dividing out the shape transforms from data merged from many nanocrystals of different sizes), assuming that certain unit-cell types are preferred. The results also suggest that the dynamic range of the data is a critical issue to be resolved in order to apply the shape transform method practically.

Original languageEnglish (US)
Pages (from-to)19-27
Number of pages9
JournalIUCrJ
Volume1
DOIs
StatePublished - Jan 1 2014

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Nanoparticles
Nanocrystals
nanocrystals
Crystals
cells
crystals
X ray lasers
Molecules
Free electron lasers
Radiation damage
Chemical modification
Protein Databases
Diffraction patterns
radiation damage
free electron lasers
dynamic range
Mathematical transformations
molecules
Scattering
surface layers

Keywords

  • nanocrystallography
  • phasing
  • shape transform
  • X-ray free electron lasers

ASJC Scopus subject areas

  • Chemistry(all)
  • Materials Science(all)
  • Condensed Matter Physics
  • Biochemistry

Cite this

Ab-initio phasing using nanocrystal shape transforms with incomplete unit cells. / Liu, Haiguang; Zatsepin, Nadia; Spence, John.

In: IUCrJ, Vol. 1, 01.01.2014, p. 19-27.

Research output: Contribution to journalArticle

Liu, Haiguang ; Zatsepin, Nadia ; Spence, John. / Ab-initio phasing using nanocrystal shape transforms with incomplete unit cells. In: IUCrJ. 2014 ; Vol. 1. pp. 19-27.
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