Evidence map›Paper›PMID 25532136›Full record

ArticleNature methods2015

Macromolecular X-ray structure determination using weak, single-wavelength anomalous data.

Gábor Bunkóczi, Airlie J McCoy, Nathaniel Echols, Ralf W Grosse-Kunstleve, Paul D Adams, James M Holton, Randy J Read, Thomas C Terwilliger

Abstract read
In one paragraph

Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.

0numbers the graph read from it
0cells of the map it votes in
23citing 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

23 citing papers in PubMed.

  1. The Untangle Challenge for accurate ensemble models.bioRxiv : the preprint server for biology · 2026
    Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Evaluating crystallographic likelihood functions using numerical quadratures.Acta crystallographica. Section D, Structural biology · 2020
    Article
  7. SAD phasing of XFEL data depends critically on the error model.Acta crystallographica. Section D, Structural biology · 2019
    Article
  8. Article
  9. Article
  10. Maximum-likelihood determination of anomalous substructures.Acta crystallographica. Section D, Structural biology · 2018
    Article
  11. The hidden treasure in your data: phasing with unexpected weak anomalous scatterers from routine data sets.Acta crystallographica. Section F, Structural biology communications · 2017
    Article
  12. Contemporary Use of Anomalous Diffraction in Biomolecular Structure Analysis.Methods in molecular biology (Clifton, N.J.) · 2017
    Review
  13. Article
  14. Merging of synchrotron serial crystallographic data by a genetic algorithm.Acta crystallographica. Section D, Structural biology · 2016
    Article
  15. Article
  16. Article
  17. Article
  18. Initiating heavy-atom-based phasing by multi-dimensional molecular replacement.Acta crystallographica. Section D, Structural biology · 2016
    Article
  19. Data-collection strategy for challenging native SAD phasing.Acta crystallographica. Section D, Structural biology · 2016
    Article
  20. Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing.Acta crystallographica. Section D, Structural biology · 2016
    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

8 authors.

Gábor BunkócziDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
Airlie J McCoyDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
Nathaniel EcholsPhysical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Ralf W Grosse-KunstlevePhysical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Paul D AdamsPhysical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
James M Holton1] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [2] Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA.
Randy J ReadDepartment of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.ORCID 0000000182730047
Thomas C TerwilligerLos Alamos National Laboratory, Los Alamos, New Mexico, USA.ORCID 0000000163840320

Funding

PROJECT 5 - DUKE - STRUCTURE VALIDATION AND IMPROVEMENT FOR PROTEINS AND N. ACIDSP01GM063210 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI ADAMS, PAUL DAVID · 2001 to 2021
$33.5M
Yeast ExpressionP50GM073210 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI STROUD, ROBERT M · 2004 to 2013
$21.5M
NIGMS NIH HHS GM073210NIGMS NIH HHS P01 GM063210NIGMS NIH HHS P01GM063210NIGMS NIH HHS P50 GM073210Wellcome Trust 082961Wellcome Trust 082961/Z/07/ZWellcome Trust 100140
6 · The paper itself

Abstract

We describe a likelihood-based method for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak anomalous signal. With the use of partial models and electron density maps in searches for anomalously scattering atoms, testing of alternative values of parameters and parallelized automated model-building, this method has the potential to extend the applicability of the SAD method in challenging cases.

Indexed as

SoftwareAlgorithmsCrystallography, X-RayLikelihood FunctionsMacromolecular SubstancesModels, MolecularSignal-To-Noise RatioMacromolecular Substances

Identifiers

PMID25532136
PMCPMC4312553

What OpenQuestion holds

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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.