A survey of global radiation damage to 15 different protein crystal types at room temperature: a new decay model

Leal, Ricardo M. F.; Bourenkov, Gleb; Russi, Silvia; Попов, А. Н.

doi:10.1107/s0909049512049114

Cited by 25 publications

(62 citation statements)

References 63 publications

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“…The collection of diffraction data continuously and at dose rates in excess of $0.7 MGy s À1 allowed more data to be collected from each crystal. In contrast, other recent studies (for example, Warkentin et al, 2013;Leal et al, 2013) conducted at lower dose rates have reported little dose-rate dependence at room temperature.…”

Section: Introductionmentioning

confidence: 65%

Exploiting fast detectors to enter a new dimension in room-temperature crystallography

Owen

Paterson

Axford

et al. 2014

Acta Cryst D Biol Crystallogr

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Section: Introductionmentioning

confidence: 65%

Exploiting fast detectors to enter a new dimension in room-temperature crystallography

Owen

Paterson

Axford

et al. 2014

Acta Cryst D Biol Crystallogr

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“…We advise that the 0.38-MGy dose limit not be exceeded when global damage is to be minimized. This dose limit holds strictly true only for tetragonal HEWL crystals at 2-Å resolution, but RT studies on other protein crystals (see above) reported D 1/2 values of the same order of magnitude ranging from 0.10 to 1.18 MGy at various resolutions and employing a variety of techniques to estimate the dose (20,23,26,32,34,35,60).…”

Section: Discussionmentioning

confidence: 99%

Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures

Mora

Coquelle

Bury

et al. 2020

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

101

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Radiation damage limits the accuracy of macromolecular structures in X-ray crystallography. Cryogenic (cryo-) cooling reduces the global radiation damage rate and, therefore, became the method of choice over the past decades. The recent advent of serial crystallography, which spreads the absorbed energy over many crystals, thereby reducing damage, has rendered room temperature (RT) data collection more practical and also extendable to microcrystals, both enabling and requiring the study of specific and global radiation damage at RT. Here, we performed sequential serial raster-scanning crystallography using a microfocused synchrotron beam that allowed for the collection of two series of 40 and 90 full datasets at 2- and 1.9-Å resolution at a dose rate of 40.3 MGy/s on hen egg white lysozyme (HEWL) crystals at RT and cryotemperature, respectively. The diffraction intensity halved its initial value at average doses (D1/2) of 0.57 and 15.3 MGy at RT and 100 K, respectively. Specific radiation damage at RT was observed at disulfide bonds but not at acidic residues, increasing and then apparently reversing, a peculiar behavior that can be modeled by accounting for differential diffraction intensity decay due to the nonuniform illumination by the X-ray beam. Specific damage to disulfide bonds is evident early on at RT and proceeds at a fivefold higher rate than global damage. The decay modeling suggests it is advisable not to exceed a dose of 0.38 MGy per dataset in static and time-resolved synchrotron crystallography experiments at RT. This rough yardstick might change for proteins other than HEWL and at resolutions other than 2 Å.

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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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A survey of global radiation damage to 15 different protein crystal types at room temperature: a new decay model

Abstract: A systematic study of the sensitivity to radiation damage of crystals held at room temperature for a large set of model macromolecular structures is presented.

Cited by 25 publications

References 63 publications

Exploiting fast detectors to enter a new dimension in room-temperature crystallography

Exploiting fast detectors to enter a new dimension in room-temperature crystallography

Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures

Predicting the X-ray lifetime of protein crystals

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