Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector

Abstract

X reveals 3D structures and elucidates functions of biomolecules with atomic resolution, thereby enabling researchers to make fundamental contributions to molecular biology and structure-based drug discovery 1. Synchrotron radiation, together with large-format 2D detectors, has been essential to the success of modern MX 2,3. In parallel with the evolution of synchrotron sources, several generations of X-ray detectors have been developed, namely, image plates 4 , multiwire proportional counters 5 , X-ray television detectors 6 , charge-coupled device (CCD) detectors 7 , and hybrid (pixel-array) photon-counting (HPC) detectors 8. Currently, most MX beamlines are equipped with HPC detectors, or are scheduled to be.

Long-wavelength native-SAD phasing: opportunities and challenges

“…Detection of low-energy photons is challenging for HPCs -the current standard in MX beamlines. The performance of the EIGER 4M detector used in this study was indeed affected by the lowest reachable energy threshold, inaccuracy in threshold calibration (Leonarski et al, 2018) and absorption from an $1 mm Al/Si layer on the surface of the silicon sensor, as well as from a protective 20 mm-thick Mylar foil. Unfortunately, the latter effect becomes more pronounced for high-angle reflections because of parallax effects but can be minimized using a curved detector (Wagner et al, 2016) or flat detectors in a Vshape configuration.…”

“…6(c)]. This is likely caused by the socalled 'corner effect' from hybrid pixel-array photon-counting detectors (HPCs), which could inflate the R meas by introducing systematic intensity-measurement errors, particularly when the detector energy threshold is above 50% as was the case at 3.3 Å (Leonarski et al, 2018). In addition, the inaccuracy of absorption correction in data processing could also reduce the accuracy of long-wavelength data.…”

Nucleobase carbonyl groups are poor Mg2+inner-sphere binders but excellent monovalent ion binders—a critical PDB survey

“…In the future, significant help in assigning solvent molecules should stem from better use of anomalous signals (Leonarski et al 2017). Thanks to continual improvements in anomalous difference measurements through specialized beamlines, constant accuracy improvement of X-ray detectors, and more efficient software (Storoni et al 2004;Thorn and Sheldrick 2011;Weinert et al 2015;Olieric et al 2016;Wagner et al 2016;Leonarski et al 2018), it might become possible to make use of weak Na + /Mg 2+ signals when high resolution is available. With greater likelihood, the detection of the anomalous signals of heavier ions such as K + , Ca 2+ , Cl − , and SO 4 2− will be facilitated (Ennifar et al 2003;Auffinger et al 2004a;Mueller-Dieckmann et al 2007;Thorn and Sheldrick 2011;Echols et al 2014;D'Ascenzo and Auffinger 2016).…”

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction

“…We made every attempt to pick conservative parameters describing the crystal size and mosaicity, the liquid and air paths, the X-ray spectrum and intensity, and the solid angle subtended by the pixel array. Although early generation XFEL imaging detectors may have lacked the large dynamic range, linear response and well characterized gain needed to achieve our goals, we estimate that current-generation devices such as the ePix (Sikorski et al, 2016), Jungfrau (Leonarski et al, 2018) and AGIPD (Allahgholi et al, 2015) offer the level of measurement stability that is incorporated into our assumptions. As for data analysis, it was important to model the contributions to each pixel from distributions of mosaic rotations and beam energies, the so-called 'ray-tracing' approach, and to properly weight the shot-noise statistical probability of each pixel value with equation (15).…”