Date Published: November 01, 2018
Publisher: International Union of Crystallography
Author(s): Naomine Yano, Taro Yamada, Takaaki Hosoya, Takashi Ohhara, Ichiro Tanaka, Nobuo Niimura, Katsuhiro Kusaka.
In this article, the status of the STARGazer data-processing software and its data-processing algorithms are described in detail. The STARGazer data-processing software is used for neutron time-of-flight single-crystal diffraction data collected using the IBARAKI Biological Crystal Diffractometer.
Hydrogen is one of the main atoms that proteins are composed of, and it plays an important role in protein function and structure. X-rays are often used to solve protein structures, but it is difficult to determine the position of H atoms without ultrahigh resolution. Additionally, because protons have no electrons, we cannot theoretically determine proton positions using X-rays. Neutron protein crystallography (NPC) is used to determine H-atom and proton positions in proteins, and plays very important roles in understanding physiological functions and reaction mechanisms (Niimura et al., 2016 ▸; O’Dell et al., 2016 ▸). Several neutron instruments for protein crystallography have been installed at research reactors that use monochromatic neutrons or relatively narrow bands of neutrons (with wavelengths from 3 to 4 Å) emitted by monochromators or multilayer band-pass filters, respectively. BIX-3 (Tanaka et al., 2002 ▸) and BIX-4 (Kurihara et al., 2004 ▸) at Japan Research Reactor No. 3 (JRR-3) and BIODIFF at the Research Neutron Source Heinz Maier-Leibnitz (FRM-II) are monochromator-type diffractometers. LADI-III (Blakeley et al., 2010 ▸) at the Institute Laue–Langevin (ILL) and IMAGINE (Munshi et al., 2011 ▸) at HFIR (High Flux Isotope Reactor) are quasi-Laue-type diffractometers. The neutron time-of-flight (TOF) method uses pulsed neutrons with continuous wavelengths generated at accelerator-driven high-intensity spallation neutron sources. Because the velocity of a neutron depends on its wavelength, the flight times of neutrons from their sources (the moderator) through the sample to the detectors vary. Thus, we can calculate the neutron wavelength by measuring the flight times, and separate diffraction peaks at the same detector pixel and different wavelengths using fixed time-resolved detectors. In this manner, the TOF method can save data-collection time compared with the monochromatic or quasi-Laue methods (Niimura & Podjarny, 2011 ▸). The IBARAKI Biological Crystal Diffractometer (iBIX; Tanaka et al., 2010 ▸; Kusaka et al., 2013 ▸) at the Japan Proton Accelerator Research Complex (J-PARC; Ikeda, 2009 ▸), the Protein Crystallography Station (PCS; Chen & Unkefer, 2017 ▸) at Los Alamos Neutron Science Center (LANSCE; Cooper, 2006 ▸) and the Macromolecular Neutron Diffractometer (MaNDi; Coates et al., 2015 ▸) at the Spallation Neutron Source (SNS; Mason et al., 2000 ▸) are TOF neutron diffractometers for NPC. Additionally, the NMX macromolecular diffractometer at the European Spallation Source (ESS; Hall-Wilton & Theroine, 2014 ▸) is under construction and will soon be operational.
iBIX has been available for user experiments since the end of 2008. To date, neutron diffraction data from many organic, inorganic and protein single crystals have been measured and reaction mechanisms have been proposed (Yokoyama et al., 2012 ▸, 2015 ▸; Ogo et al., 2013 ▸; Unno et al., 2015 ▸; Nakamura et al., 2015 ▸). Thus, it appears that STARGazer works well as TOF NPC diffraction data-processing software.
In the future, the accelerator power of J-PARC will be increased to a maximum of 1 MW. We will be able to collect diffraction data from crystals with larger unit cells. We will continue to develop STARGazer to make it easier to use and will obtain more accurate intensity data. Examples of this include the automation of data processing and the modification of the PeakIntegration component to implement a peak-deconvolution procedure for overlapped peaks from crystals with larger unit cells.