Evidence map›Paper›PMID 22628654›Full record

ArticleScience (New York, N.Y.)2012

Linking crystallographic model and data quality.

P Andrew Karplus, Kay Diederichs

Abstract read
In one paragraph

Article in Science (New York, N.Y.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,214 papers.

0numbers the graph read from it
0cells of the map it votes in
1,214citing 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

1,214 citing papers in PubMed.

  1. Article
  2. Article
  3. Crystal structures of the sweet-tasting protein honey truffle active component from Mattirolomyces terfezioides.Acta crystallographica. Section F, Structural biology communications · 2026
    Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Scotty: lattice coincidences for macromolecular crystallographic phasing.Acta crystallographica. Section D, Structural biology · 2026
    Article
  14. Article
  15. Article
  16. ThebioRxiv : the preprint server for biology · 2026
    Article
  17. Article
  18. Article
  19. Article
  20. Article

1,154 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

2 authors.

P Andrew KarplusDepartment of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
Kay Diederichs

Funding

NUTRITIONAL REGULATION OF CYSTEINE DIOXYGENASER01DK056649 · NIDDK · CORNELL UNIVERSITY ITHACA · PI STIPANUK, MARTHA H · 2000 to 2013
$4.0M
Improving Modeling by Learning from Details of High Accuracy Protein StructuresR01GM083136 · NIGMS · OREGON STATE UNIVERSITY · PI KARPLUS, PAUL ANDREW · 2008 to 2015
$1.7M
NIDDK NIH HHS DK056649NIDDK NIH HHS R01 DK056649NIGMS NIH HHS GM083136NIGMS NIH HHS R01 GM083136
6 · The paper itself

Abstract

In macromolecular x-ray crystallography, refinement R values measure the agreement between observed and calculated data. Analogously, R(merge) values reporting on the agreement between multiple measurements of a given reflection are used to assess data quality. Here, we show that despite their widespread use, R(merge) values are poorly suited for determining the high-resolution limit and that current standard protocols discard much useful data. We introduce a statistic that estimates the correlation of an observed data set with the underlying (not measurable) true signal; this quantity, CC*, provides a single statistically valid guide for deciding which data are useful. CC* also can be used to assess model and data quality on the same scale, and this reveals when data quality is limiting model improvement.

Indexed as

Crystallography, X-RayModels, MolecularProtein ConformationCysteine DioxygenaseData Interpretation, StatisticalProteinsResearch DesignCysteine DioxygenaseProteins

Identifiers

PMID22628654
PMCPMC3457925

What OpenQuestion holds

Textmetadata
LicenceTDM
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.