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. 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.
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Nicole M
authors.initials: NM
authors.lastname: Scarborough
authors.affiliation: Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: G M Dilshan P
authors.initials: GM
authors.lastname: Godaliyadda
authors.affiliation: Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Dong Hye
authors.initials: DH
authors.lastname: Ye
authors.affiliation: GM/CA@APS, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Kissick
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Shijie
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Justin A
authors.initials: JA
authors.lastname: Newman
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Sheedlo
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Azhad U
authors.initials: AU
authors.lastname: Chowdhury
authors.affiliation: GM/CA@APS, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA.
authors.forename: Robert F
authors.initials: RF
authors.lastname: Fischetti
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Chittaranjan
authors.initials: C
authors.lastname: Das
authors.affiliation: Department of Mathematics, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Gregery T
authors.initials: GT
authors.lastname: Buzzard
authors.affiliation: Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Charles A
authors.initials: CA
authors.lastname: Bouman
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Garth J
authors.initials: GJ
authors.lastname: Simpson
mesh_terms: D003460:Crystallization; D018360:Crystallography, X-Ray; D046911:Macromolecular Substances; D011506:Proteins / Q000737:chemistry*; D017356:Synchrotrons; D014961:X-Ray Diffraction
chemical_list: D046911:Macromolecular Substances; D011506:Proteins
keywords: X-ray diffraction; dynamic sampling; nonlinear optical microscopy; second-harmonic generation; supervised learning approach; two-photon-excited fluorescence