Evidence map›Paper›PMID 23254653›Full record

ArticleJournal of synchrotron radiation2013

To scavenge or not to scavenge, that is STILL the question.

Elizabeth G Allan, Melissa C Kander, Ian Carmichael, Elspeth F Garman

Abstract read
In one paragraph

Article in Journal of synchrotron radiation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

17 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Using sound pulses to solve the crystal-harvesting bottleneck.Acta crystallographica. Section D, Structural biology · 2018
    Article
  7. Estimate your dose: RADDOSE-3D.Protein science : a publication of the Protein Society · 2018
    Article
  8. Article
  9. Objective evaluation of radiation damage in a nucleoprotein complex.Acta crystallographica. Section D, Structural biology · 2016
    Article
  10. RNA protects a nucleoprotein complex against radiation damage.Acta crystallographica. Section D, Structural biology · 2016
    Article
  11. Article
  12. Article
  13. Challenges and solutions for the analysis of in situ, in crystallo micro-spectrophotometric data.Acta crystallographica. Section D, Biological crystallography · 2015
    Article
  14. Review
  15. Diffraction before destruction.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2014
    Article
  16. Article
  17. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Elizabeth G AllanLaboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
Melissa C Kander
Ian Carmichael
Elspeth F Garman

Funding

Wellcome TrustWellcome Trust 088287/Z/09/Z
6 · The paper itself

Abstract

An extensive radiation chemistry literature would suggest that the addition of certain radical scavengers might mitigate the effects of radiation damage during protein crystallography diffraction data collection. However, attempts to demonstrate and quantify such an amelioration and its dose dependence have not yielded consistent results, either at room temperature (RT) or 100 K. Here the information thus far available is summarized and reasons for this lack of quantitative success are identified. Firstly, several different metrics have been used to monitor and quantify the rate of damage, and, as shown here, these can give results which are in conflict regarding scavenger efficacy. In addition, significant variation in results from data collected from crystals treated in nominally the same way has been observed. Secondly, typical crystallization conditions contain substantial concentrations of chemical species which already interact strongly with some of the X-ray-induced radicals that the added scavengers are intended to intercept. These interactions are probed here by the complementary technique of on-line microspectrophotometry carried out on solutions and crystals held both at 100 K and RT, the latter enabled by the use of a beamline-mounted humidifying device. With the help of computational chemistry, attempts are made to assign some of the characteristic spectral features observed experimentally. A further source of uncertainty undoubtedly lies in the challenge of reliably measuring the parameters necessary for the accurate calculation of the absorbed dose (e.g. crystal size and shape, beam profile) and its distribution within the volume of the crystal (an issue addressed in detail in another article in this issue). While microspectrophotometry reveals that the production of various species can be quenched by the addition of scavengers, it is less clear that this observation can be translated into a significant gain in crystal dose tolerance for macromolecular crystallographers.

Indexed as

AnimalsBuffersChickensCrystallizationCrystallography, X-RayEgg WhiteFree Radical ScavengersInformaticsMuramidaseNitratesProteinsBuffersFree Radical ScavengersMuramidaseNitratesProteins

Identifiers

PMID23254653
PMCPMC3526919

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.