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

Abstract

Single-wavelength anomalous dispersion (SAD) utilizing anomalous signal from native S atoms, or other atoms withZ≤ 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 drivede novostructure 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 thef'' 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 thatSHELXDwas 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 anomalousmore » scatterers such as Cl, Ca, Mnetc., checking for the presence of fortuitous anomalous signal in data from well diffracting crystals could prove useful in either determining the structurede novoor in accurately assigning surface-bound atoms.« less

Authors:
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Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL), Upton, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1409626
Report Number(s):
BNL-114678-2017-JA¿¿¿
Journal ID: ISSN 2053-230X; ACSFEN
DOE Contract Number:  
SC0012704
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section F, Structural Biology Communications; Journal Volume: 73; Journal Issue: 4
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES

Citation Formats

Hegde, Raghurama P., Fedorov, Alexander A., Sauder, J. Michael, Burley, Stephen K., Almo, Steven C., and Ramagopal, Udupi A. The hidden treasure in your data: phasing with unexpected weak anomalous scatterers from routine data sets. United States: N. p., 2017. Web. doi:10.1107/S2053230X17002680.
Hegde, Raghurama P., Fedorov, Alexander A., Sauder, J. Michael, Burley, Stephen K., Almo, Steven C., & Ramagopal, Udupi A. The hidden treasure in your data: phasing with unexpected weak anomalous scatterers from routine data sets. United States. doi:10.1107/S2053230X17002680.
Hegde, Raghurama P., Fedorov, Alexander A., Sauder, J. Michael, Burley, Stephen K., Almo, Steven C., and Ramagopal, Udupi A. Wed . "The hidden treasure in your data: phasing with unexpected weak anomalous scatterers from routine data sets". United States. doi:10.1107/S2053230X17002680.
@article{osti_1409626,
title = {The hidden treasure in your data: phasing with unexpected weak anomalous scatterers from routine data sets},
author = {Hegde, Raghurama P. and Fedorov, Alexander A. and Sauder, J. Michael and Burley, Stephen K. and Almo, Steven C. and Ramagopal, Udupi A.},
abstractNote = {Single-wavelength anomalous dispersion (SAD) utilizing anomalous signal from native S atoms, or other atoms withZ≤ 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 drivede novostructure 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 thef'' 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 thatSHELXDwas 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, Mnetc., checking for the presence of fortuitous anomalous signal in data from well diffracting crystals could prove useful in either determining the structurede novoor in accurately assigning surface-bound atoms.},
doi = {10.1107/S2053230X17002680},
journal = {Acta Crystallographica. Section F, Structural Biology Communications},
number = 4,
volume = 73,
place = {United States},
year = {Wed Mar 22 00:00:00 EDT 2017},
month = {Wed Mar 22 00:00:00 EDT 2017}
}