Title: Dynamic X-ray diffraction sampling for protein crystal positioning

Abstract

A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction, significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Furthermore, by usingin situtwo-photon-excited fluorescence microscopy measurementsmore » as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by limiting the dose and area exposed for image reconstruction and crystal positioning using data collection hardware present in most macromolecular crystallography end-stations.« less

Authors:

Scarborough, Nicole M. ^[1]; Godaliyadda, G. M. Dilshan P. ^[2]; Ye, Dong Hye  ^[2];

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Kissick, David J. ^[3]; Zhang, Shijie ^[1]; Newman, Justin A. ^[1]; Sheedlo, Michael J. ^[1]; Chowdhury, Azhad U. ^[1]; Fischetti, Robert F. ^[3]; Das, Chittaranjan ^[1]; Buzzard, Gregery T. ^[4]; Bouman, Charles A. ^[2]; Simpson, Garth J. ^[1]

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+ Show Author Affiliations

1. Purdue Univ., West Lafayette, IN (United States). Dept. of Chemistry
2. Purdue Univ., West Lafayette, IN (United States). Dept. of Electrical and Computer Engineering
3. Argonne National Lab. (ANL), Argonne, IL (United States). X-ray Science Division
4. Purdue Univ., West Lafayette, IN (United States). Dept. of Mathematics

Publication Date:

Sun Jan 01 00:00:00 EST 2017

Research Org.:

Argonne National Lab. (ANL), Argonne, IL (United States)

Sponsoring Org.:

US Air Force Office of Scientific Research (AFOSR); National Institutes of Health (NIH)

OSTI Identifier:

1390796

Grant/Contract Number:  

AC02-06CH11357; R01GM-103910; R01GM-103410

Resource Type:

Accepted Manuscript

Journal Name:

Journal of Synchrotron Radiation (Online)

Additional Journal Information:

Journal Name: Journal of Synchrotron Radiation (Online); Journal Volume: 24; Journal Issue: 1; Journal ID: ISSN 1600-5775

Publisher:

International Union of Crystallography

Country of Publication:

United States

Language:

English

Subject:

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND TECHNOLOGY; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; X-ray diffraction; dynamic sampling; nonlinear optical microscopy; second-harmonic generation; supervised learning approach; two-photon-excited fluorescence