1. Reconstructing three-dimensional protein crystal intensities from sparse unoriented two-axis X-ray diffraction patterns
- Author
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Ti-Yen Lan, Hugh T. Philipp, Sol M. Gruner, Mark W. Tate, Veit Elser, and Jennifer L. Wierman
- 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 - 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., 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.
- Published
- 2017
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