Development of data processing software for a new TOF single crystal neutron diffractometer at J-PARC

Hydrogen-bond network and pH sensitivity in transthyretin: Neutron crystal structure of human transthyretin

“…The exposure times were 22 h for each set at 120 kW J-PARC accelerator power and 12 h at 220 kW. The collected data were indexed, integrated and scaled up to 2.0 Å resolution with STARGazer which was developed for iBIX time-of-flight diffraction data processing (Ohhara et al, 2009). Under the data processing, the diffraction spots from the edge of the wavelength (2.7-3.2 and 6.2-6.7) were excluded, because disk chopper is not fully open at the edge of the wavelength band.…”

Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX

“…The number of observed neutrons at x, y , and t corresponding to the horizontal and vertical detector positions ( x, y ) and a time-of-flight channel ( t ) are recorded. The procedure after this is similar to monochromatic methods and includes peak searching, determination of initial UB matrix, peak indexing, refinement of UB matrix, and peak integration12. Because the number of observed neutrons at each pixel of the peak position of three-dimensional (3D) data was insufficient to fit functions accurately, we used projections of the 3D peak in the direction of the TOF axis to improve the statistical precision.…”

“…4. Intensity statistics, with peaks I/σ(I ) larger than 0, were calculated using the iBIX data processing software STARGazer program12, and joint refinements of neutron and X-ray data were carried out using the PHENIX program40. In order to evaluate the algorithm utility, the intensity and refinement data statistics of the profile fitting method were compared to those of the summation integration method implemented in STARGazer by using the same integration regions, peaks and initial refinement model.…”

“…TOF neutron protein crystallography (NPC) diffraction data processing software has been developed at each diffractometer facility independently. STARGazer12, d*TREK modified for wavelength-resolved Laue neutron crystallography13, and Mantid14 are used at iBIX, PCS, and MaNDi, respectively. Overall, the data quality indices R merge and R pim 15 of TOF NPC diffraction data are higher than monochromatic synchrotron X-ray and nuclear reactor neutron diffraction data161718192021222324.…”

Materials and Life Science Experimental Facility (MLF) at the Japan Proton Accelerator Research Complex II: Neutron Scattering Instruments

“…If the accelerator power were to reach 1 MW, the total measurement time or the sample size will be reduced by half. To improve the quality of the integrated intensity of weak reflections, we developed a profile-fitting method for the peak integration of the data reduction software STARGazer [100]. The integrated intensities and model structure obtained using the profile-fitting method were more accurate than those obtained using the summation integration method, especially in the case of higher-resolution shells [101].…”