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Reconstructing three-dimensional protein crystal intensities from sparse unoriented two-axis X-ray diffraction patterns
- Source :
- Journal of Applied Crystallography
- Publication Year :
- 2017
- Publisher :
- International Union of Crystallography (IUCr), 2017.
-
Abstract
- To simulate the signal level of serial microcrystallography experiments at storage ring sources, data frames were collected from a large lysozyme crystal rotated about two orthogonal axes and illuminated by a dim X-ray source. Using the EMC algorithm, this study shows that three-dimensional intensity reconstruction is still feasible even without the knowledge of the crystal orientation in each data frame.<br />Recently, there has been a growing interest in adapting serial microcrystallography (SMX) experiments to existing storage ring (SR) sources. For very small crystals, however, radiation damage occurs before sufficient numbers of photons are diffracted to determine the orientation of the crystal. The challenge is to merge data from a large number of such ‘sparse’ frames in order to measure the full reciprocal space intensity. To simulate sparse frames, a dataset was collected from a large lysozyme crystal illuminated by a dim X-ray source. The crystal was continuously rotated about two orthogonal axes to sample a subset of the rotation space. With the EMC algorithm [expand–maximize–compress; Loh & Elser (2009). Phys. Rev. E, 80, 026705], it is shown that the diffracted intensity of the crystal can still be reconstructed even without knowledge of the orientation of the crystal in any sparse frame. Moreover, parallel computation implementations were designed to considerably improve the time and memory scaling of the algorithm. The results show that EMC-based SMX experiments should be feasible at SR sources.
- Subjects :
- 0301 basic medicine
Diffraction
sparse data
Photon
X-ray serial microcrystallography
Addenda and Errata
01 natural sciences
General Biochemistry, Genetics and Molecular Biology
Crystal
03 medical and health sciences
synchrotron radiation sources
Optics
protein microcrystallography
0103 physical sciences
010306 general physics
Scaling
Sparse matrix
Physics
business.industry
Research Papers
Reciprocal lattice
030104 developmental biology
Orthogonal coordinates
EMC algorithm
X-ray crystallography
business
Subjects
Details
- ISSN :
- 16005767
- Volume :
- 50
- Database :
- OpenAIRE
- Journal :
- Journal of Applied Crystallography
- Accession number :
- edsair.doi.dedup.....7321be6293dbfbe38f009389e93feee1
- Full Text :
- https://doi.org/10.1107/s1600576717006537