Evidence map›Paper›PMID 25286840›Full record

ArticleActa crystallographica. Section D, Biological crystallography2014

Multi-crystal native SAD analysis at 6 keV.

Qun Liu, Youzhong Guo, Yanqi Chang, Zheng Cai, Zahra Assur, Filippo Mancia, Mark I Greene, Wayne A Hendrickson

Abstract read
In one paragraph

Article in Acta crystallographica. Section D, Biological crystallography, 2014. 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. xia2.multiplex: a multi-crystal data-analysis pipeline.Acta crystallographica. Section D, Structural biology · 2022
    Article
  3. Current research in structural biology · 2021
    Article
  4. Article
  5. Article
  6. Making routine native SAD a reality: lessons from beamline X06DA at the Swiss Light Source.Acta crystallographica. Section D, Structural biology · 2019
    Article
  7. Article
  8. Article
  9. 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
  10. Article
  11. Article
  12. Article
  13. Data-collection strategy for challenging native SAD phasing.Acta crystallographica. Section D, Structural biology · 2016
    Article
  14. Progress in protein crystallography.Protein and peptide letters · 2016
    Article
  15. Crystallographic phasing from weak anomalous signals.Current opinion in structural biology · 2015
    Review
  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

8 authors.

Qun LiuNYCOMPS, New York Structural Biology Center, New York, NY 10032, USA.
Youzhong GuoNYCOMPS, New York Structural Biology Center, New York, NY 10032, USA.
Yanqi ChangNYCOMPS, New York Structural Biology Center, New York, NY 10032, USA.
Zheng CaiDepartment of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Zahra AssurDepartment of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
Filippo ManciaDepartment of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
Mark I GreeneDepartment of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Wayne A HendricksonNYCOMPS, New York Structural Biology Center, New York, NY 10032, USA.

Funding

Structural Genomics on Membrane ProteinsU54GM095315 · NIGMS · NEW YORK STRUCTURAL BIOLOGY CENTER · PI ROST, BURKHARD · 2010 to 2014
$15.2M
Proposal for an Administrative Supplement for Equipment Purchases for NIGMS Awardees NOT-GM-18-022R01GM107462 · NIGMS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI HENDRICKSON, WAYNE A. · 2014 to 2021
$3.6M
CysZ proteins_A family of sulfate transporters with remarkable architectureR01GM098617 · NIGMS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI MANCIA, FILIPPO · 2012 to 2016
$1.6M
NIGMS NIH HHS GM095315NIGMS NIH HHS GM098617NIGMS NIH HHS GM107462NIGMS NIH HHS R01 GM098617NIGMS NIH HHS R01 GM107462NIGMS NIH HHS U54 GM095315
6 · The paper itself

Abstract

Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in de novo structure determination. Here, native SAD procedures are described to enhance signal to noise in anomalous diffraction by using multiple crystals in combination with synchrotron X-rays at 6 keV. Increased anomalous signals were obtained at 6 keV compared with 7 keV X-ray energy, which was used for previous native SAD analyses. A feasibility test of multi-crystal-based native SAD phasing was performed at 3.2 Å resolution for a known tyrosine protein kinase domain, and real-life applications were made to two novel membrane proteins at about 3.0 Å resolution. The three applications collectively serve to validate the robust feasibility of native SAD phasing at lower energy.

Indexed as

Protein ConformationBacillus subtilisBacterial ProteinsCrystallography, X-RayErbB ReceptorsHumansListeria monocytogenesMembrane Transport ProteinsModels, MolecularProtein Structure, TertiaryReproducibility of ResultsSynchrotronsBacterial ProteinsErbB ReceptorsMembrane Transport Proteinsanomalous diffractionlight-atom-only native SADphase determinationprotein structure

Identifiers

PMID25286840
PMCPMC4188002

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Registered trials

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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.