Experimental procedure for the characterization of radiation damage in macromolecular crystals

Leal, Ricardo M. F.; Bourenkov, Gleb; Svensson, Olof; Spruce, Darren; Guijarro, Matias; Попов, А. Н.

doi:10.1107/s0909049511002251

Cited by 22 publications

(27 citation statements)

References 33 publications

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“…This procedure research papers requires the sacrifice of a whole crystal or part of a crystal. It involves measuring the degree of damage in a sample, or part of it, by repeated exposure of the crystal to X-rays (Leal et al, 2011). Such a protocol to determine the radiation sensitivity of a crystal has been established and implemented in DAWB.…”

Section: Crystal Radiation-sensitivity Measurement Workflowmentioning

confidence: 99%

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography

Brockhauser

Svensson

Bowler

et al. 2012

Acta Crystallogr D Biol Cryst

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Section: Crystal Radiation-sensitivity Measurement Workflowmentioning

confidence: 99%

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography

Brockhauser

Svensson

Bowler

et al. 2012

Acta Crystallogr D Biol Cryst

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“…In other words, a macromolecular crystal can only withstand a certain amount of X-ray dose before it is destroyed as a result of radiation damage. Therefore, obtaining accurate and complete diffraction data sets of macromolecular crystals within their lifetime is very important (Gonzá lez, 2003;Leal, 2011;Yang et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

A multi-dataset data-collection strategy produces better diffraction data

Liu

Chen²,

et al. 2011

Acta Crystallogr A Found Crystallogr

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A multi-dataset (MDS) data-collection strategy is proposed and analyzed for macromolecular crystal diffraction data acquisition. The theoretical analysis indicated that the MDS strategy can reduce the standard deviation (background noise) of diffraction data compared with the commonly used single-dataset strategy for a fixed X-ray dose. In order to validate the hypothesis experimentally, a data-quality evaluation process, termed a readiness test of the X-ray data-collection system, was developed. The anomalous signals of sulfur atoms in zinc-free insulin crystals were used as the probe to differentiate the quality of data collected using different data-collection strategies. The datacollection results using home-laboratory-based rotating-anode X-ray and synchrotron X-ray systems indicate that the diffraction data collected with the MDS strategy contain more accurate anomalous signals from sulfur atoms than the data collected with a regular data-collection strategy. In addition, the MDS strategy offered more advantages with respect to radiation-damage-sensitive crystals and better usage of rotating-anode as well as synchrotron X-rays.

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“…A prerequisite to optimizing the experimental protocol is knowing the effective crystal lifetime available for data collection. Diffracted intensity is known to decay with dose (6,7), relative B factor B rel is known to increase (8), and protocols exist for determining dose tolerance under carefully controlled conditions (9). However, when collecting data with the goal of solving challenging new structures, these results are often of limited use (10), because the optimally efficient even-dose case (11) is often not experimentally achievable.…”

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confidence: 99%

Predicting the X-ray lifetime of protein crystals

Zeldin

Brockhauser

Bremridge

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Radiation damage is a major cause of failure in macromolecular crystallography experiments. Although it is always best to evenly illuminate the entire volume of a homogeneously diffracting crystal, limitations of the available equipment and imperfections in the sample often require a more sophisticated targeting strategy, involving microbeams smaller than the crystal, and translations of the crystal during data collection. This leads to a highly inhomogeneous distribution of absorbed X-rays (i.e., dose). Under these common experimental conditions, the relationship between dose and time is nonlinear, making it difficult to design an experimental strategy that optimizes the radiation damage lifetime of the crystal, or to assign appropriate dose values to an experiment. We present, and experimentally validate, a predictive metric diffraction-weighted dose for modeling the rate of decay of total diffracted intensity from protein crystals in macromolecular crystallography, and hence we can now assign appropriate "dose" values to modern experimental setups. Further, by taking the ratio of total elastic scattering to diffraction-weighted dose, we show that it is possible to directly compare potential data-collection strategies to optimize the diffraction for a given level of damage under specific experimental conditions. As an example of the applicability of this method, we demonstrate that by offsetting the rotation axis from the beam axis by 1.25 times the full-width half maximum of the beam, it is possible to significantly extend the dose lifetime of the crystal, leading to a higher number of diffracted photons, better statistics, and lower overall radiation damage.G iven an adequately diffracting crystal, radiation damage is the dominant cause of failure for macromolecular crystallography (MX) experiments (1), and overcoming this problem has been one of the major motivations for the development of new methods. By way of illustration: over the last 11 years at beamline 8.3.1 of the Advanced Light Source (ALS), more than 1,000 structures have been solved and deposited into the Protein Data Bank, but more than 25,000 datasets were collected. Similar dataset-to-deposition ratios have been reported elsewhere (2, 3). A retrospective analysis of the ALS 8.3.1 data reveals that radiation damage played a dominant role in the failure to obtain phases for structure solution by anomalous dispersion methods. Indeed, if radiation damage did not exist, investigators could simply keep collecting data until any desired signal-to-noise ratio was attained.Much of the recent excitement over serial femtosecond crystallography with X-ray Free Electron Lasers (XFELs) has been due to the vast gains in the diffraction/damage ratios demonstrated (4). Despite these major advances, the technology for these systems is not yet mature, and the linear nature of the XFEL facilities limits the number of end stations, greatly reducing capacity compared with a traditional synchrotron source. Synchrotron-based MX is thus likely to remain the dominant ...

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Experimental procedure for the characterization of radiation damage in macromolecular crystals

Cited by 22 publications

References 33 publications

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography

A multi-dataset data-collection strategy produces better diffraction data

Predicting the X-ray lifetime of protein crystals

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