Diffraction data analysis in the presence of radiation damage

Abstract

In macromolecular crystallography, the acquisition of a complete set of diffraction intensities typically involves a high cumulative dose of X-ray radiation. In the process of data acquisition, the irradiated crystal lattice undergoes a broad range of chemical and physical changes. These result in the gradual decay of diffraction intensities, accompanied by changes in the macroscopic organization of crystal lattice order and by localized changes in electron density that, owing to complex radiation chemistry, are specific for a particular macromolecule. The decay of diffraction intensities is a well defined physical process that is fully correctable during scaling and merging analysis and therefore, while limiting the amount of diffraction, it has no other impact on phasing procedures. Specific chemical changes, which are variable even between different crystal forms of the same macromolecule, are more difficult to predict, describe and correct in data. Appearing during the process of data collection, they result in gradual changes in structure factors and therefore have profound consequences in phasing procedures. Examples of various combinations of radiation-induced changes are presented and various considerations pertinent to the determination of the best strategies for handling diffraction data analysis in representative situations are discussed.

Structural and Kinetic Effects on Changes in the CO2 Binding Pocket of Human Carbonic Anhydrase II

“…This implies that increasing X-ray dose led to enzyme activation perhaps producing active hydroxyl radicals, which would allow for reaction with CO 2 leading to the formation of bicarbonate, as discussed by Sjoblom et al (7). Radiation damage is a common issue known to impact macromolecular structures under crystallographic conditions, so this behavior between electrons and water molecules is not unlikely (27-30). The absorbed dose at which Sjoblom et al observed bicarbonate was approximately 6 × 10 6 Gy, and the occupancies were 65% CO 2 and 35% bicarbonate.…”

Crystal Structure of Cardiac Troponin C Regulatory Domain in Complex with Cadmium and Deoxycholic Acid Reveals Novel Conformation

“…Diffraction images were processed with HKL3000. The merging of data sets and corrections for radiation-induced effects were performed using a novel hierarchical procedure 18 , 45 . Heavy atom position search was performed at 2.8 Å with SHELXD 46 .…”

Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data

“…To detect radiation damage in single-crystal data sets, the R d plot (Diederichs, 2006), anomalous correlation coefficient, scaling B factor and R merge may all be useful, as have been thoroughly reviewed (Dauter, 2006b;Garman & Nave, 2009;Garman, 2010;Borek et al, 2010). For multi-crystal native SAD experiments, these indicators are also effective to detect and reject seriously damaged frames.…”