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Native SAD is maturing.

Rose JP, Wang BC, Weiss MS - IUCrJ (2015)

Bottom Line: These atoms include sodium, magnesium, phosphorus, sulfur, chlorine, potassium and calcium.Native SAD phasing is challenging and is critically dependent on the collection of accurate data.This article will focus on advances that have caught the attention of the community over the past five years.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia, USA.

ABSTRACT
Native SAD phasing uses the anomalous scattering signal of light atoms in the crystalline, native samples of macromolecules collected from single-wavelength X-ray diffraction experiments. These atoms include sodium, magnesium, phosphorus, sulfur, chlorine, potassium and calcium. Native SAD phasing is challenging and is critically dependent on the collection of accurate data. Over the past five years, advances in diffraction hardware, crystallographic software, data-collection methods and strategies, and the use of data statistics have been witnessed which allow 'highly accurate data' to be routinely collected. Today, native SAD sits on the verge of becoming a 'first-choice' method for both de novo and molecular-replacement structure determination. This article will focus on advances that have caught the attention of the community over the past five years. It will also highlight both de novo native SAD structures and recent structures that were key to methods development.

No MeSH data available.


A plot of the number of native SAD structures deposited per year in the Protein Data Bank. The number shown include both de novo structures and previously solved structures that have been redetermined as part of software and methods development. Excluded from the list are standard proteins such as insulin, lysozyme, thaumatin, trypsin and glucose isomerase. The peak in native SAD structure determinations during the period from 2004 to 2009 reflects, among other things, the introduction of the Rigaku chromium-rotating anode, which was used by the SECSG (Adams et al., 2003 ▸) and SGC (Yakunin et al., 2004 ▸) structural genomics centers, and the work carried out by Cheng Yang at Rigaku and Nobuhisa Watanabe at Hokkaido University, Japan. The large spike in PDB entries in 2006 reflects ten structures reported in a methods-development paper (Mueller-Dieckmann et al., 2007 ▸), which first noted that chloride, sulfate, phosphate or metal ions present in the crystal can contribute to the anomalous signal in the data. The large increase in PDB depositions for 2014 reflects the proteins used for the development of multi-data-set averaging (from single or multiple crystals) methods, with 11 structures representing the SLS studies reported in 2014 (Weinert et al., 2015 ▸).
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fig1: A plot of the number of native SAD structures deposited per year in the Protein Data Bank. The number shown include both de novo structures and previously solved structures that have been redetermined as part of software and methods development. Excluded from the list are standard proteins such as insulin, lysozyme, thaumatin, trypsin and glucose isomerase. The peak in native SAD structure determinations during the period from 2004 to 2009 reflects, among other things, the introduction of the Rigaku chromium-rotating anode, which was used by the SECSG (Adams et al., 2003 ▸) and SGC (Yakunin et al., 2004 ▸) structural genomics centers, and the work carried out by Cheng Yang at Rigaku and Nobuhisa Watanabe at Hokkaido University, Japan. The large spike in PDB entries in 2006 reflects ten structures reported in a methods-development paper (Mueller-Dieckmann et al., 2007 ▸), which first noted that chloride, sulfate, phosphate or metal ions present in the crystal can contribute to the anomalous signal in the data. The large increase in PDB depositions for 2014 reflects the proteins used for the development of multi-data-set averaging (from single or multiple crystals) methods, with 11 structures representing the SLS studies reported in 2014 (Weinert et al., 2015 ▸).

Mentions: Today, there are close to 150 de novo native SAD structures in the Protein Data Bank (Fig. 1 ▸), which recently announced its 108 000th structure. However, advances in technology and methodology during the past five years in the areas of X-ray sources, detectors, sample preparation, data-collection strategies, data reduction, phasing and structure solution, as discussed below, show great promise in making native SAD phasing a routine approach for macromolecular structure determination.


Native SAD is maturing.

Rose JP, Wang BC, Weiss MS - IUCrJ (2015)

A plot of the number of native SAD structures deposited per year in the Protein Data Bank. The number shown include both de novo structures and previously solved structures that have been redetermined as part of software and methods development. Excluded from the list are standard proteins such as insulin, lysozyme, thaumatin, trypsin and glucose isomerase. The peak in native SAD structure determinations during the period from 2004 to 2009 reflects, among other things, the introduction of the Rigaku chromium-rotating anode, which was used by the SECSG (Adams et al., 2003 ▸) and SGC (Yakunin et al., 2004 ▸) structural genomics centers, and the work carried out by Cheng Yang at Rigaku and Nobuhisa Watanabe at Hokkaido University, Japan. The large spike in PDB entries in 2006 reflects ten structures reported in a methods-development paper (Mueller-Dieckmann et al., 2007 ▸), which first noted that chloride, sulfate, phosphate or metal ions present in the crystal can contribute to the anomalous signal in the data. The large increase in PDB depositions for 2014 reflects the proteins used for the development of multi-data-set averaging (from single or multiple crystals) methods, with 11 structures representing the SLS studies reported in 2014 (Weinert et al., 2015 ▸).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4491315&req=5

fig1: A plot of the number of native SAD structures deposited per year in the Protein Data Bank. The number shown include both de novo structures and previously solved structures that have been redetermined as part of software and methods development. Excluded from the list are standard proteins such as insulin, lysozyme, thaumatin, trypsin and glucose isomerase. The peak in native SAD structure determinations during the period from 2004 to 2009 reflects, among other things, the introduction of the Rigaku chromium-rotating anode, which was used by the SECSG (Adams et al., 2003 ▸) and SGC (Yakunin et al., 2004 ▸) structural genomics centers, and the work carried out by Cheng Yang at Rigaku and Nobuhisa Watanabe at Hokkaido University, Japan. The large spike in PDB entries in 2006 reflects ten structures reported in a methods-development paper (Mueller-Dieckmann et al., 2007 ▸), which first noted that chloride, sulfate, phosphate or metal ions present in the crystal can contribute to the anomalous signal in the data. The large increase in PDB depositions for 2014 reflects the proteins used for the development of multi-data-set averaging (from single or multiple crystals) methods, with 11 structures representing the SLS studies reported in 2014 (Weinert et al., 2015 ▸).
Mentions: Today, there are close to 150 de novo native SAD structures in the Protein Data Bank (Fig. 1 ▸), which recently announced its 108 000th structure. However, advances in technology and methodology during the past five years in the areas of X-ray sources, detectors, sample preparation, data-collection strategies, data reduction, phasing and structure solution, as discussed below, show great promise in making native SAD phasing a routine approach for macromolecular structure determination.

Bottom Line: These atoms include sodium, magnesium, phosphorus, sulfur, chlorine, potassium and calcium.Native SAD phasing is challenging and is critically dependent on the collection of accurate data.This article will focus on advances that have caught the attention of the community over the past five years.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia, USA.

ABSTRACT
Native SAD phasing uses the anomalous scattering signal of light atoms in the crystalline, native samples of macromolecules collected from single-wavelength X-ray diffraction experiments. These atoms include sodium, magnesium, phosphorus, sulfur, chlorine, potassium and calcium. Native SAD phasing is challenging and is critically dependent on the collection of accurate data. Over the past five years, advances in diffraction hardware, crystallographic software, data-collection methods and strategies, and the use of data statistics have been witnessed which allow 'highly accurate data' to be routinely collected. Today, native SAD sits on the verge of becoming a 'first-choice' method for both de novo and molecular-replacement structure determination. This article will focus on advances that have caught the attention of the community over the past five years. It will also highlight both de novo native SAD structures and recent structures that were key to methods development.

No MeSH data available.