The absorption factor for a cylindrical specimen perpendicular to a cylindrical beam of the same radius. Application to the X-ray study of CsDNA with the use of synchrotron radiation

Abstract

An X‐ray diffraction study of CsDNA has been carried out with the use of synchrotron radiation of wavelength λ = 1.2 Å. The geometry corresponds to a cylindrical specimen brought into a cylindrical beam of the same diameter and the absorption factor and the primary‐beam attenuation factor have been calculated as functions of specimen μR for this geometry. The optimum size of a specimen is here about 1.5 times greater than that in the case of a plane‐parallel beam used in International Tables for X‐ray Crystallography [Vol. II, (1967), 2nd ed., p. 295. Birmingham: Kynoch Press]. Experimental and calculated primary‐beam attenuation factors have been compared and the experimental value of the linear absorption coefficient μ of CsDNA has been estimated for various humidities. The agreement between μc = 78.1 and μo = 78.2 ± 3.6 cm−1 (relative humidity 66–75%) indicates that the geometrical model used is suitable to describe polymer fibres in a cylindrical beam of nearly the same size. It is seen from the observed μ values that there is one caesium ion per nucleotide (monomer unit of DNA molecule) in the specimens used.

Attenuation corrections for X-ray and neutron fibre diffraction studies

“…Fig. 2 shows that, for cylindrical samples, as #R increases, 7~ increases more with w but remains relatively independent of n. In the arrangement described by Skuratovskii et al (1978), the total reflected energy, E, is proportional to A(h)(#R) z and is maximum when #R ~ 2.1. In the arrangement considered here, there is no optimum value for #R since E is increased by increasing the length of fibre in the beam.…”

“…The transmission factor for cylindrical samples has been considered for diffraction in the equatorial plane (International Tables for X-ray Crystallography , 1985;Rouse, Cooper, York & Chakera, 1970) and off the equatorial plane when the diameter of the sample is matched by that of the X-ray or neutron beam (Skuratovskii, Kapitonova & Volkova, 1978). We consider the arrangement in which the irradiated sample volume corresponds to that of a long cylinder, radius R, with the incident beam perpendicular to the cylinder axis ( Fig.…”

“…Attenuation effects are particularly pronounced for cylindrical samples in X-ray studies of fibres containing heavily absorbing alkali-metal ions. For example, for the Cs salt of DNA, # = 78.1 cm-~ at A = 1.2/~, (Skuratovskii et al, 1978) and, for the TI salt, /z = 121 cm -~ at A = 1.5/~, (Langan, Forsyth, Mahendrasingam, Alexeev et al, 1992). The typical radial dimension of a DNA fibre is ,,~100p.m, which corresponds to a value of 0.6 for #R. In this case, AMc(h) and o<(h) agree to better than 1%, AMc(h) and A0 differ by up to 7%, and AMc(h) and values tabulated by Skuratovskii et al differ by more than 5% within the scattering angle of 35 ° .…”

Synchrotron Radiation and Crystallography: the First 50 Years

“…À1 ] mrad À2 mm À2 have now been reported from ESRF (see Elleaume et al, 1998). such as DESY in Hamburg, SPEAR in Stanford, NINA in Daresbury and VEPP in Novosibirsk. These machines had high¯uxes into the hard X-ray range and enabled pioneering experiments, for example in protein crystallography, including multiple-wavelength anomalous dispersion (Phillips et al, 1976;Webb et al, 1977;Harmsen et al, 1976;Helliwell, 1984), energy-dispersive diffraction (Bordas et al, 1976, Buras & Gerward, 1975, EXAFS (Stern et al, 1975), biological small-angle diffraction (Haslegrove et al, 1977), DNA ®bre diffraction (Skuratovskii et al, 1978), and so on. Historical insights into the performances of these machines, from the current perspective, are described in detail for example by Huxley & Holmes (1997) at DESY, Munro (1997) at Daresbury and Doniach et al (1997) at Stanford.…”