A limited-range step-scan method for collecting X-ray diffraction data

Hanson, Jonathan C.; Watenpaugh, Keith David; Sieker, L.C.; Jensen, L. H.

doi:10.1107/s0567739479001443

Cited by 44 publications

(17 citation statements)

References 5 publications

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“…These data were then reduced to integrated intensities using the procedure of Hanson et al 21 , which fits gaussian profiles over smoothly varying backgrounds. Standard corrections were made for Lorentz and polarization factors, absorption 22 and scale 23 .…”

Section: Diffraction Measurementsmentioning

confidence: 99%

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Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulphur

Hendrickson

Teeter

1981

Nature

654

512

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The highly ordered crystal structure of crambin has been solved at 1.5 Å resolution directly from the diffraction data of a native crystal at a wavelength remote from the sulphur absorption edge. The molecule has three disulphide bridges among its 46 amino acid residues, of which 46% are in helices and 17% are in a β-sheet. Crambin is shown to be an amphipathic protein, inasmuch as its six charged groups are segregated from hydrophobic surface elements. Phasing methods used here will also apply elsewhere.Bijvoet's observation 1 that anomalous scattering might aid in solving the phase problem has had many implications 2 , including suggestions that departures from Friedel's law of diffraction symmetry might suffice to determine directly the atomic structures of crystals containing heavy atoms [3][4][5] . Anomalous-scattering methods have also been widely used in protein crystallography [6][7][8][9][10][11] , particularly as an adjunct to isomorphous-replacement phasing. We have now combined elements from these two traditions to solve the structure of crambin by exploiting the anomalous scattering of sulphur atoms at a single wavelength (1.54 Å of CuKα) far removed from the absorption edge of sulphur (5.02 Å).Crambin is a small protein found in the embryonic tissue (cotyledons and hypocotyledons) of seeds from Crambe abyssinica, a relative of mustard and rape commonly known as Abyssinian cabbage. It is hydrophobic in that organic solvents are required to solubilize it, Van Etten et al. 12 characterized crambin after noticing that crystals formed during evaporation of an aqueous acetone extract of defatted seed meal. The remarkable crystalline order observed by Teeter for this protein (strong diffraction from spacings <0.88 Å) 13 correlates well with the unprecedented structural stability seen in solution by Llinás et al. 14 using NMR spectroscopy. The function of crambin is not known. However, the recently completed chemical sequence 15 reveals an unmistakable homology with the plant toxins purothionin 16 and viscotoxin 17 . Crambin itself is not toxic when fed to rats 18 .We set out to solve the crystal structure of crambin in view of its exceptional potential for providing detailed structural information and in the hope of shedding light on the function of this hydrophobic protein. When our efforts to prepare heavy-atom derivatives failed, we explored alternatives to isomorphous replacement for phase determination. Our experience HHS Public Access Author Manuscript Author ManuscriptAuthor ManuscriptAuthor Manuscript in using anomalous scattering to locate the iron atoms in myohaemerythrin 19 led us to contemplate an attempt based on the six sulphur atoms in crambin. An estimate of the magnitude of Bijvoet differences to be expected from crambin gave a value about half that found with myohaemerythrin and showed that sulphur scattering would account for 98% of the expected anomalous signal. The expected contribution of the sulphur partial structure to the protein diffraction pattern proved to be 29% (〈|F ...

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Section: Diffraction Measurementsmentioning

confidence: 99%

“…Two of the three aromatic residues are within 4° of the expected transverse conformation at χ 2 , but Tyr 29 has χ 2 = 55°. The disulphide torsion angles, which are also expected to favour ±90°, are −79° (3-40), 106° (4-32) and −86° (16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26).…”

Section: Molecular Conformationmentioning

confidence: 99%

Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulphur

Hendrickson

Teeter

1981

Nature

654

512

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“…The 09--20 step-scan technique (Hanson, Watenpaugh, Sieker & Jensen, 1979) was used to collect data at a rate of approximately 3000 reflections per day. Backgrounds were assumed to be a function only of 0 and representative values were obtained at the end of data collection by counting pseudo-reflections between the reciprocal-lattice rows.…”

Section: Data Collection and Processingmentioning

confidence: 99%

Restrained least-squares refinement of Themiste dyscritum methydroxohemerythrin at 2.0 Å resolution

Stenkamp¹,

Sieker²,

Jensen³

1982

Acta Crystallogr Sect B

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A model of methydroxohemerythrin has been refined at 2.0/k resolution to clarify the structure of the binuclear iron complex in this oxygen-transport protein. An effort was made to minimize the crystallographic bias introduced by the assumed model by omitting the binuclear complex from the initial model and rebuilding it during the refinement. The procedure is extensively described, and some troublesome aspects of the refinement are indicated. The final R is 0.187 for 32254 reflections with d spacings in the range 10-2-0 ,/~.

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“…Wyckoff, Doscher, Tsernoglou, Inagami, Johnson, Hardman, Allwell, Kelly & Richards, 1967;Hanson, Watenpaugh, Sieker & Jensen, 1979). These usually combine a limited number of counting steps in the region of the peak maximum with some form of averaged background; this is frequently assumed to be a function of 20 only and is estimated by scanning between reciprocal-lattice rows, although local empirical corrections may be necessary (Hanson, Watenpaugh, Sieker & Jensen, 1979). Our method could operate similarly, but we prefer to measure some background in each scan to avoid assumptions about its behaviour; an accurate value is particularly important in the estimation of weak reflections.…”

Section: Discussionmentioning

confidence: 99%

“…More recently, Hanson, Watenpaugh, Sieker & Jensen (1979) have reported a method which may be thought of as an approximation to Diamond's (1969) method and to the one that we present below. It is a two-pass procedure which fits Gaussian peak shapes to the vectors of counts.…”

Section: Var[i(e)ljl=p + [W/(n--w)12 (B + B2) (14)mentioning

confidence: 99%