Economic Sociology

Dauter, Luke

doi:10.4135/9781412952613.n152

Cited by 19 publications

(26 citation statements)

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“…Zn, Mg, Se, they can usually be located by inserting anomalous difference magnitudes into a direct-methods procedure. With very precise data, even lighter atoms such as S and Cl can be picked up in this way (Dauter et al, 1999(Dauter et al, , 2000. The separations of the anomalous scatterers are usually large enough for them to be located with less than atomic resolution data.…”

Section: Experimentally Positioned Anomalous Scatterersmentioning

confidence: 99%

ACORN: a review

Yao

Dodson

Wilson

et al. 2006

Acta Crystallogr D Biol Crystallogr

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The ACORN system was originally developed as a means of ab initio solution of protein structures when atomic resolution data were available. The first step is to obtain a starting set of phases, which must be at least slightly better than random. These may be calculated from a fragment of the structure, which can be anything from a single metal atom to a complete molecular-replacement model. A number of standard procedures are available in ACORN to orientate and position such a fragment. The fragment provides initial phases that give the first of a series of maps that are iteratively refined by a dynamic density-modification (DDM) process. Another FFTbased procedure is Sayre-equation refinement (SER), which modifies phases better to satisfy the Sayre equation. With good-quality atomic resolution data, the final outcome of applying DDM and SER is a map similar in appearance to that found from a refined structure, which is readily interpreted by automated procedures. Further development of ACORN now enables structures to be solved with less than atomic resolution data. A critical part of this development is the artificial extension of the data from the observed limit to 1 Å resolution. These extended reflections are allocated unit normalized structure amplitudes and then treated in a similar way to observed reflections except that they are downweighted in the calculation of maps. ACORN maps, especially at low resolution, tend to show C atoms less well, in particular C atoms which fall within the first diffraction minimum of their three neighbours. Two new density-modification procedures (DDM1 and DDM2) and a density-enhancement procedure (ENH) have been devised to counter this problem. It is demonstrated that high-quality maps showing individual atoms can be produced with the new ACORN. ACORN has also been demonstrated to be very effective in refining phase sets derived from physical processes such as those using anomalous scattering or isomorphous derivative data. Future work will be directed towards applying ACORN to resolutions down to 2 Å .

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Section: Experimentally Positioned Anomalous Scatterersmentioning

confidence: 99%

ACORN: a review

Yao

Dodson

Wilson

et al. 2006

Acta Crystallogr D Biol Crystallogr

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show abstract

“…For the atoms C, N, O and S, the magnitude of the anomalous signal is negligible and usually ignored. However, anomalous scattering from sulfur has been successfully used to obtain phase information in a number of cases (Hendrickson & Teeter, 1981;Dauter et al, 1999). Anomalous scattering effects are more easily detectable for heavier atoms.…”

Section: Overviewmentioning

confidence: 99%

MAD data collection – current trends

Walsh

Evans

Sanishvili

et al. 1999

Acta Crystallogr D Biol Cryst

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The multiwavelength anomalous dispersion (MAD) method of protein structure determination is becoming a routine technique in protein crystallography. The increased number of wavelength-tuneable synchrotron beamlines capable of performing challenging MAD experiments, coupled with the widespread availability of charge-coupled device (CCD) based X-ray detectors with fast read-out times have brought MAD structure determination to a new exciting level. Ultrafast MAD data collection is now possible and, with the widespread use of selenium in the form of selenomethionine for phase determination, the method is growing in popularity. Recent developments in crystallographic software are complementing the above advances, paving the way for rapid protein structure determination. An overview of a typical MAD experiment is described, with emphasis on the rates and quality of data acquisition now achievable at third-generation synchrotron sources.

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“…Usually, experimenters find a lower signal than they expected, particularly if the data quality is not very high. Sometimes surprises happen when the crystal contains some additional unexpected scatterers such as, for example, chloride ions in addition to the ten expected S atoms in the crystal of hen egg-white lysozyme (Dauter et al, 1999).…”

Section: Introductionmentioning

confidence: 99%

“…They can be reasonably well estimated for highly redundant data, but for data measured from low-symmetry crystals with low redundancy it is difficult to be sure that all uncertainties are statistically valid. The importance of properly estimated uncertainties has been discussed in several texts on data-collection strategy (Dauter et al, 1999;Borek et al, 2003;Evans, 2006).…”

Section: Introductionmentioning

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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Economic Sociology

Cited by 19 publications

References 0 publications

ACORN: a review

ACORN: a review

MAD data collection – current trends

Estimation of anomalous signal in diffraction data

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