Anomalous signal indicators in protein crystallography

Zwart, Peter H.

doi:10.1107/s0907444905023589

Cited by 41 publications

(59 citation statements)

References 62 publications

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“…Because these programs are implemented primarily as Python modules, complex data including models, reflections and other viewable data may be exchanged with the GUI without resorting to parsing log files. The current PHENIX release (version 1.5) includes GUIs for phenix.refine (Afonine et al, 2005), phenix.xtriage (Zwart et al, 2005), the AutoSol , AutoBuild and LigandFit (Terwilliger et al, 2006) wizards, the restraints editor REEL, all of the validation tools and several utilities for creating and manipulating maps and reflection files. More recent builds of PHENIX contain a new GUI for the AutoMR wizard and future releases will include a new interface for Phaser .…”

Section: Graphical User Interfacementioning

confidence: 99%

“…A comprehensive tool for analyzing X-ray diffraction data is phenix.xtriage (Zwart et al, 2005), which carries out tests ranging from space-group determination and detection of twinning to detection of anomalous signal. These tests provide the user and the various wizards with a set of statistics that characterize a data set.…”

Section: Analysis Of Experimental Datamentioning

confidence: 99%

See 1 more Smart Citation

PHENIX: a comprehensive Python-based system for macromolecular structure solution

Adams¹,

Afonine²,

Bunkóczi³

et al. 2012

International Tables for Crystallography

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5,428

6,848

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Section: Graphical User Interfacementioning

confidence: 99%

Section: Analysis Of Experimental Datamentioning

confidence: 99%

PHENIX: a comprehensive Python-based system for macromolecular structure solution

Adams¹,

Afonine²,

Bunkóczi³

et al. 2012

International Tables for Crystallography

Self Cite

5,428

6,848

View full text Add to dashboard Cite

“…The Bijvoet ratio (similarly to R anom ) increases towards unity if the amplitudes are aberrated with errors and its absolute value is not a good indicator of the anomalous signal (Zwart, 2005). However, a comparison of the observed and theoretically calculated Bijvoet ratio is quite informative (Dauter et al, 2002).…”

Section: Bijvoet Amplitude Ratiomentioning

confidence: 99%

Estimation of anomalous signal in diffraction data

Dauter

2006

Acta Crystallogr D Biol Crystallogr

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It is difficult to judge objectively the amount and resolution limit of the anomalous signal present in diffraction data. While several criteria can be used for this purpose, the usefulness of these indicators varies and depends on factors such as the data redundancy, the accuracy of the estimation of intensities and their uncertainties, and the properties of the anomalously scattering atoms in the crystal. Various indicators give an approximate measure of the anomalous signal, but do not provide a reliable guarantee that the crystal structure will be solved. The ultimate criterion of the anomalous signal is a successful structure solution. The current data‐acquisition and phasing methods are so advanced that it is often possible to phase reflections and obtain preliminary electron‐density maps in a few minutes, while the crystal still resides at the experimental station and further data can be collected if necessary.

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“…Zwart [121] discussed quality metrics applied to anomalous data in order to predict success or failure of phasing attempts. Sorted intensity data from XPREP output in scalepack format was used to calculate the anomalous signal:noise ratio:…”

Section: Measurabilitymentioning

confidence: 99%

Phosphorus SAD Phasing for Nucleic Acid Structures: Limitations and Potential

2016

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Phasing of nucleic acid crystal diffraction data using the anomalous signal of phosphorus, P-SAD, at Cuk α wavelength has been previously demonstrated using Z-DNA. Since the original work on P-SAD with Z-DNA there has been, with a notable exception, a conspicuous absence of applications of the technique to additional nucleic acid crystal structures. We have reproduced the P-SAD phasing of Z-DNA using a rotating-anode source and have attempted to phase a variety of nucleic acid crystals using P-SAD without success. A comparison of P-SAD using Z-DNA and a representative nucleic acid, the Dickerson-Drew dodecamer, is presented along with a S-SAD using only two sulfurs to phase a 2'-thio modified DNA decamer. A theoretical explanation for the limitation of P-SAD applied to nucleic acids is presented to show that the relatively high atomic displacement parameter of phosphorus in the nucleic acid backbone is responsible for the lack of success in applying P-SAD to nucleic acid diffraction data.

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Anomalous signal indicators in protein crystallography

Cited by 41 publications

References 62 publications

PHENIX: a comprehensive Python-based system for macromolecular structure solution

PHENIX: a comprehensive Python-based system for macromolecular structure solution

Estimation of anomalous signal in diffraction data

Phosphorus SAD Phasing for Nucleic Acid Structures: Limitations and Potential

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