Crop yield loss due to flooding is a threat to food security. Submergence-induced hypoxia in plants results in stabilization of group VII ETHYLENE RESPONSE FACTORs (ERF-VIIs), which aid survival under these adverse conditions. ERF-VII stability is controlled by the N-end rule pathway, which proposes that ERF-VII N-terminal cysteine oxidation in normoxia enables arginylation followed by proteasomal degradation. The PLANT CYSTEINE OXIDASEs (PCOs) have been identified as catalysts of this oxidation. ERF-VII stabilization in hypoxia presumably arises from reduced PCO activity. We directly demonstrate that PCO dioxygenase activity produces Cys-sulfinic acid at the N terminus of an ERF-VII peptide, which then undergoes efficient arginylation by an arginyl transferase (ATE1). This provides molecular evidence of N-terminal Cys-sulfinic acid formation and arginylation by N-end rule pathway components, and a substrate of ATE1 in plants. The PCOs and ATE1 may be viable intervention targets to stabilize N-end rule substrates, including ERF-VIIs, to enhance submergence tolerance in agriculture.

We present the current status of RADDOSE-3D, a software tool allowing the estimation of the dose absorbed in a macromolecular crystallography diffraction experiment. The code allows a temporal and spatial dose contour map to be calculated for a crystal of any geometry and size as it is rotated in an X-ray beam, and gives several summary dose values: among them diffraction weighted dose. This allows experimenters to plan data collections which will minimize radiation damage effects by spreading the absorbed dose more homogeneously, and thus to optimize the use of their crystals. It also allows quantitative comparisons between different radiation damage studies, giving a universal "x-axis" against which to plot various metrics.

Radiation damage analysis with experimental SAXS data allows for the quantitative comparison of the efficacy of various additive radioprotectant compounds. Relevant extensions to RADDOSE-3D and the creation of a new visualization library to enable this study are presented.

Radiation damage remains one of the major limitations to accurate structure determination in protein crystallography (PX). Despite the use of cryo-cooling techniques, it is highly probable that a number of the structures deposited in the Protein Data Bank (PDB) have suffered substantial radiation damage as a result of the high flux densities of third generation synchrotron X-ray sources. Whereas the effects of global damage upon diffraction pattern reflection intensities are readily detectable, traditionally the (earlier onset) site-specific structural changes induced by radiation damage have proven difficult to identify within individual PX structures. More recently, however, development of the B Damage metric has helped to address this problem. B Damage is a quantitative, peratom metric identifies potential sites of specific damage by comparing the atomic B-factor values of atoms that occupy a similar local packing density environment in the structure. Building upon this past work, this article presents a program, RABDAM, to calculate the B Damage metric for all selected atoms within any standard-format PDB or mmCIF file. RABDAM provides several useful outputs to assess the extent of damage suffered by an input PX structure. This free and open-source software will allow assessment and improvement of the quality of PX structures both previously and newly deposited in the PDB.

X-ray crystallography is the most common technique for the determination of three-dimensional crystalline structures at the atomic scale. Since the discovery of the diffraction of X-rays by crystals over one hundred years ago, the technique has developed into an indispensable tool for material scientists and structural biologists worldwide. In this review, several milestones in the development of X-ray crystallography are presented, along with many of the Nobel laureates that made significant contributions to the success of the method. We conclude with a look at the current challenges in the field and speculate on the ensuing major developments that could lead to the next Nobel Prize related to X-ray crystallography.

Radiation damage is one of the major limiting factors for crystallographers trying to collect useful data during macromolecular X-ray crystallography (MX) experiments at third generation synchrotron sources [1]. The dose received by the crystal has long been thought to be a good indicator of the extent of the global radiation damage, however it is only recently that adequate tools have been established to allow us to accurately measure the dose distribution within a crystal during an MX experiment. Analysis of various dose metrics described in [2], has resulted in us developing a new way of quantifying dose for unevenly irradiated crystals: the Diffraction Weighted Dose (DWD). Experiments conducted by Zeldin et al. (unpublished) were performed to test the robustness of this dose metric at describing the damage observed under different dose contrast regimes for fifteen different cubic insulin crystals. The resolution dependent form of the intensity decay with the DWD is explored here. Our findings confirm that the decay of diffracted intensity is exponential as a function of the DWD where the decay rate is dependent on the diffraction angle. Comparison of these findings with the room temperature (RT) dose decay models (DDM) proposed by Blake and Phillips [3] (and extended by Hendrickson (1976) [4]) and also Leal et al. [5] are tested against the data to determine whether their RT DDMs can be extended to describe resolution dependent diffraction intensity loss at cryotemperatures (100K). Results of these comparisons show consistencies in the exponential form of the relationship between the diffracted intensities and the diffraction angle, and give some information on more appropriate DDMs that might be applicable across the entire range of intensity loss. These findings will be presented.

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