Evidence map›Paper›PMID 28368276›Full record

ArticleActa crystallographica. Section F, Structural biology communications2017

The hidden treasure in your data: phasing with unexpected weak anomalous scatterers from routine data sets.

Raghurama P Hegde, Alexander A Fedorov, J Michael Sauder, Stephen K Burley, Steven C Almo, Udupi A Ramagopal

Abstract read
In one paragraph

Article in Acta crystallographica. Section F, Structural biology communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

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0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Current research in structural biology · 2021
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4 · The record

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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

6 authors.

Raghurama P HegdeDivision of Biological Sciences, Poornaprajna Institute of Scientific Research, #4, 16th Cross, Sadashivnagar, Bangalore 560 080, India.
Alexander A FedorovDepartment of Biochemistry, Albert Einstein College of Medicine, Ullmann Building, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, New York, NY 10461, USA.
J Michael SauderLilly Biotechnology Center, Eli Lilly and Company, 10290 Campus Point Drive, San Diego, CA 92121, USA.
Stephen K BurleyRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers University, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA.
Steven C AlmoDepartment of Biochemistry, Albert Einstein College of Medicine, Ullmann Building, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, New York, NY 10461, USA.
Udupi A RamagopalDivision of Biological Sciences, Poornaprajna Institute of Scientific Research, #4, 16th Cross, Sadashivnagar, Bangalore 560 080, India.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Single-wavelength anomalous dispersion (SAD) utilizing anomalous signal from native S atoms, or other atoms with Z ≤ 20, generally requires highly redundant data collected using relatively long-wavelength X-rays. Here, the results from two proteins are presented where the anomalous signal from serendipitously acquired surface-bound Ca atoms with an anomalous data multiplicity of around 10 was utilized to drive de novo structure determination. In both cases, the Ca atoms were acquired from the crystallization solution, and the data-collection strategy was not optimized to exploit the anomalous signal from these scatterers. The X-ray data were collected at 0.98 Å wavelength in one case and at 1.74 Å in the other (the wavelength was optimized for sulfur, but the anomalous signal from calcium was exploited for structure solution). Similarly, using a test case, it is shown that data collected at ∼1.0 Å wavelength, where the f'' value for sulfur is 0.28 e, are sufficient for structure determination using intrinsic S atoms from a strongly diffracting crystal. Interestingly, it was also observed that SHELXD was capable of generating a substructure solution from high-exposure data with a completeness of 70% for low-resolution reflections extending to 3.5 Å resolution with relatively low anomalous multiplicity. Considering the fact that many crystallization conditions contain anomalous scatterers such as Cl, Ca, Mn etc., checking for the presence of fortuitous anomalous signal in data from well diffracting crystals could prove useful in either determining the structure de novo or in accurately assigning surface-bound atoms.

Indexed as

AnimalsArchaeal ProteinsBacterial ProteinsCalciumCations, DivalentChickensCloning, MolecularCrystallizationCrystallography, X-RayEgg ProteinsEscherichia coliGene ExpressionGenetic VectorsMuramidaseProtein ConformationPseudomonas syringaeArchaeal ProteinsBacterial ProteinsCalciumCations, DivalentEgg ProteinsMuramidaseRecombinant ProteinsSulfurSAD phasingweak anomalous signal

Identifiers

PMID28368276
PMCPMC5379167

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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.