The probability distribution of X-ray intensities

Wilson, A. J. C.

doi:10.1107/s0365110x49000813

Cited by 537 publications

(360 citation statements)

References 2 publications

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“…The temperature factors derived from the refined models for lysozyme (Pike & Acharya, 1994), ribonuclease, and DHFR all significantly decrease when a denaturant is added. If high resolution data are available, the temperature factor can also be estimated directly from the data using a Wilson plot (Wilson, 1949). The B-factor from the Wilson plot is 15.9 A2 for wild-type ribonuclease and 1 1.3 A2 for the data set derived from ribonuclease crystals soaked in guanidinium.…”

Section: 'C Fmentioning

confidence: 99%

The effect of denaturants on protein structure

et al. 1997

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Virtually all studies of the protein-folding reaction add either heat, acid, or a chemical denaturant to an aqueous protein solution in order to perturb the protein structure. When chemical denaturants are used, very high concentrations are usually necessary to observe any change in protein structure. In a solution with such high denaturant concentrations, both the structure of the protein and the structure of the solvent around the protein can be altered. X-ray crystallography is the obvious experimental technique to probe both types of changes. In this paper, we report the crystal structures of dihydrofolate reductase with urea and of ribonuclease A with guanidinium chloride. These two classic denaturants have similar effects on the native structure of the protein. The most important change that occurs is a reduction in the overall thermal factor. These structures offer a molecular explanation for the reduction in mobility. Although the reduction is observed only with the native enzyme in the crystal, a similar decrease in mobility has also been observed in the unfolded state in solution (Makhatadze G, Privalov PL. 1992. Protein interactions with urea and guanidinium chloride: A calorimetric study. J Mol B i d 226491-505).Keywords: denaturants; dihydrofolate reductase; protein mobility; ribonuclease A Despite our routine use of them, our understanding of the molecular mechanism by which chemical denaturants like urea or guanidinium (Gua) cause a protein to unfold is still rather limited. As has been pointed out by others (Schellman, 1987), part of the problem is that it is difficult to measure binding constants when the protein concentration is M and the denaturant concentration is 4 M. High precision scanning calorimetry has provided one experimental solution to this problem (Makhatadze & Privalov, 1992) but relating the thermodynamic data produced in such an experiment to protein structure can be difficult (Alber, 1989). While it does seem clear that denaturants interact directly with the protein (Simpson & Kauzmann, 1953), it is also clear that at high concentrations these molecules can cause substantial changes to the behavior of the solvent itself (Breslow & Guo, 1990 teins by migrating into the interior of the protein and forming hydrogen bonds to atoms in the backbone (Hedwig et al., 1991). In support of such a model, the exchange rates of some peptide NH protons, which are found on both the surface and the interior of a protein, are decreased in the presence of urea (Kim & Woodward, 1993). In addition, crystallographic studies of diketopiperazine and urea show hydrogen bonding between the amide groups and the urea (Thayer et al., 1993). Other models have suggested that denaturants act by decreasing the hydrophobic effect (Wetlaufer et al., 1964;Roseman & Jencks, 1975), which, in this instance, is usually postulated to be the dominant force stabilizing protein structure. Finally, experiments by Kim and Woodward (1 993) clearly show that, in addition to interacting with peptide bonds, urea alters...

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Section: 'C Fmentioning

confidence: 99%

The effect of denaturants on protein structure

et al. 1997

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“…In some cases, an overestimation of the nominal resolution can also be identi®ed based on the appearance of the Wilson (1949) plot of the data set. In particular, a clear deviation of the plot from linearity at the high-resolution side is often a good indication.…”

Section: The Quality Indicatorsmentioning

confidence: 99%

Global indicators of X-ray data quality

Weiss¹

2001

J Appl Crystallogr

668

564

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Global indicators of the quality of diffraction data are presented and discussed, and are evaluated in terms of their performance with respect to various tasks. Based on the results obtained, it is suggested that some of the conventional indicators still in use in the crystallographic community should be abandoned, such as the nominal resolution d min or the merging R factor R merge , and replaced by more objective and more meaningful numbers, such as the effective optical resolution d eff,opt and the redundancy-independent merging R factor R r.i.m. . Furthermore, it is recommended that the precision-indicating merging R factor R p.i.m. should be reported with every diffraction data set published, because it describes the precision of the averaged measurements, which are the quantities normally used in crystallography as observables.

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“…3b) and with a p.d.f, which is closest in its shape to the ideal acentric p.d.f. (Wilson, 1949). The effects of heavy atoms occupying only special positions, the light ones remaining in the general positions, are here also very pronounced.…”

Section: Resultsmentioning

confidence: 64%

Exact random-walk models in crystallographic statistics. IV. P.d.f.'s ofEallowing for atoms in special positions

Shmueli¹,

Weiss²

1988

Acta Cryst Sect A

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The effect of scatterers, located in variable special positions, on the probability density function of the magnitude of the normalized structure factor has been investigated. Exact characteristic functions have been obtained for all the statistically different variable special positions in triclinic, monoclinic and orthorhombic space groups except in Fdd2 and in the space groups based on the point group 222, and the probability density functions have been evaluated from their Fourier or Fourier-Bessel series expansions. It is seen that the effect of heavy scatterers, located in the special positions investigated, is very marked and should be accounted for in cases of space-group ambiguities.

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The probability distribution of X-ray intensities

Cited by 537 publications

References 2 publications

The effect of denaturants on protein structure

The effect of denaturants on protein structure

Global indicators of X-ray data quality

Exact random-walk models in crystallographic statistics. IV. P.d.f.'s ofEallowing for atoms in special positions

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