Evidence map›Paper›PMID 30291262›Full record

ArticleScientific reports2018

Pathological macromolecular crystallographic data affected by twinning, partial-disorder and exhibiting multiple lattices for testing of data processing and refinement tools.

Ivan Campeotto, Andrey Lebedev, Antoine M M Schreurs, Loes M J Kroon-Batenburg, Edward Lowe, Simon E V Phillips, Garib N Murshudov, Arwen R Pearson

Abstract read
In one paragraph

Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

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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

9 citing papers in PubMed.

  1. Article
  2. Deciphering the crystal structure of a novel nanobody against the NEIL1 DNA glycosylase.Acta crystallographica. Section D, Structural biology · 2024
    Article
  3. Making your raw data available to the macromolecular crystallography community.Acta crystallographica. Section F, Structural biology communications · 2023
    Article
  4. PAIREF: paired refinement also for Phenix users.Acta crystallographica. Section F, Structural biology communications · 2021
    Article
  5. Article
  6. Optimizing the refinement of merohedrally twinned P6Acta crystallographica. Section D, Structural biology · 2020
    Article
  7. Article
  8. Article
  9. Supercell refinement: a cautionary tale.Acta crystallographica. Section D, Structural biology · 2019
    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.

Ivan CampeottoAstbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. ivan.campeotto@leicester.ac.uk.ORCID http://orcid.org/0000-0002-0814-619X
Andrey LebedevResearch Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxford, OX11 OFA, UK.ORCID http://orcid.org/0000-0003-2261-0945
Antoine M M SchreursDepartment of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
Loes M J Kroon-BatenburgDepartment of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
Edward LoweBiochemistry Department, Oxford University, South Parks Road, Oxford, OX1 1HY, UK.
Simon E V PhillipsAstbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.ORCID http://orcid.org/0000-0001-8922-0250
Garib N MurshudovStructural Studies Division, MRC-LMB, Francis Crick Avenue, Cambridge, CB2 0QH, UK.ORCID http://orcid.org/0000-0001-6483-3587
Arwen R PearsonAstbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. arwen.pearson@cfel.de.ORCID http://orcid.org/0000-0001-8499-7490

Funding

Medical Research Council MC_UP_A025_1012Wellcome Trust
6 · The paper itself

Abstract

Twinning is a crystal growth anomaly, which has posed a challenge in macromolecular crystallography (MX) since the earliest days. Many approaches have been used to treat twinned data in order to extract structural information. However, in most cases it is usually simpler to rescreen for new crystallization conditions that yield an untwinned crystal form or, if possible, collect data from non-twinned parts of the crystal. Here, we report 11 structures of engineered variants of the E. coli enzyme N-acetyl-neuraminic lyase which, despite twinning and incommensurate modulation, have been successfully indexed, solved and deposited. These structures span a resolution range of 1.45-2.30 Å, which is unusually high for datasets presenting such lattice disorders in MX and therefore these data provide an excellent test set for improving and challenging MX data processing programs.

Indexed as

CrystallizationCrystallography, X-RayDatabases, ProteinEscherichia coliModels, MolecularOxo-Acid-LyasesProtein ConformationN-acetylneuraminate lyaseOxo-Acid-Lyases

Identifiers

PMID30291262
PMCPMC6173773

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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.