Dynamic X-ray diffraction sampling for protein crystal positioning

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• 作者：Nicole M. Scarborough ; G. M. Dilshan P. Godaliyadda ; Dong Hye Ye ; David J. Kissick ; Shijie Zhang ; Justin A. Newman ; Michael J. Sheedlo ; Azhad U. Chowdhury ; Robert F. Fischetti ; Chittaranjan Das ; Gregery T. Buzzard ; Charles A. Bouman and Garth J. Simpson
• 关键词：dynamic sampling ; supervised learning approach ; X-ray diffraction ; nonlinear optical microscopy ; two-photon-excited fluorescence ; second-harmonic generation
• 刊名：Journal of Synchrotron Radiation
• 出版年：2017
• 出版时间：January 2017
• 年：2017
• 卷：24
• 期：1
• 页码：188-195
• 全文大小：662K
• ISSN：1600-5775

文摘

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. Using in situ two-photon-excited fluorescence microscopy measurements 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.