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Journal ArticleDOI

A semi-empirical method of absorption correction

01 May 1968-Acta Crystallographica Section A (International Union of Crystallography)-Vol. 24, Iss: 3, pp 351-359
TL;DR: An extension of Furnas's method is described in this paper, where the variation of intensity of an axial reflection as the crystal is rotated about the goniometer axis is used to give a curve of relative transmission T against azimuthal angle ϕ for the corresponding reciprocal lattice level.
Abstract: An extension of Furnas's method is described. The variation of intensity of an axial reflection as the crystal is rotated about the goniometer axis is used to give a curve of relative transmission T against azimuthal angle ϕ for the corresponding reciprocal lattice level. Transmission coefficients for any general reflexion hkl are then given approximately by T(hkl) = [T(ϕinc) + T(ϕret)]/2 where ϕinc and ϕret are the azimuthal angles of the incident and reflected beams. Equations are derived for (ϕinc and ϕret and the accuracy of the method is discussed.
Citations
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Journal ArticleDOI
TL;DR: A detailed comparison of single-crystal diffraction data collected with Ag Kα and Mo’™Kα microsources (IµS) indicates that the Ag”Kα data are better when absorption is significant.
Abstract: The quality of diffraction data obtained using silver and molybdenum microsources has been compared for six model compounds with a wide range of absorption factors. The experiments were performed on two 30 W air-cooled Incoatec IµS microfocus sources with multilayer optics mounted on a Bruker D8 goniometer with a SMART APEX II CCD detector. All data were analysed, processed and refined using standard Bruker software. The results show that Ag Kα radiation can be beneficial when heavy elements are involved. A numerical absorption correction based on the positions and indices of the crystal faces is shown to be of limited use for the highly focused microsource beams, presumably because the assumption that the crystal is completely bathed in a (top-hat profile) beam of uniform intensity is no longer valid. Fortunately the empirical corrections implemented in SADABS, although originally intended as a correction for absorption, also correct rather well for the variations in the effective volume of the crystal irradiated. In three of the cases studied (two Ag and one Mo) the final SHELXL R1 against all data after application of empirical corrections implemented in SADABS was below 1%. Since such corrections are designed to optimize the agreement of the intensities of equivalent reflections with different paths through the crystal but the same Bragg 2θ angles, a further correction is required for the 2θ dependence of the absorption. For this, SADABS uses the transmission factor of a spherical crystal with a user-defined value of μr (where μ is the linear absorption coefficient and r is the effective radius of the crystal); the best results are obtained when r is biased towards the smallest crystal dimension. The results presented here suggest that the IUCr publication requirement that a numerical absorption correction must be applied for strongly absorbing crystals is in need of revision.

2,639 citations


Cites background or methods from "A semi-empirical method of absorpti..."

  • ...…Q( r, 2 ), where is the linear absorption coefficient and r the effective radius of the crystal: Icorrected ¼ Iraw SðnÞPðu; v;wÞQð r; 2 Þ: ð1Þ Similar approximations were used by Kopfmann & Huber (1968), North et al. (1968) and Huber & Kopfmann (1969) and in many subsequent papers and programs....

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  • ...The empirical or multiscan correction involves refining the incident beam scale factors and spherical harmonic coefficients so that the intensities of equivalent reflections become more equal (Kopfmann & Huber, 1968; North et al., 1968; Blessing, 1995)....

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  • ...The SADABS program (Bruker, 2014) assumes that the corrected intensity is given by the product of an incident beam scale factor S(n), where n is the frame number, a diffracted beam factor P(u, v, w), where u, v and w are the direction cosines of the diffracted beam relative to crystal-fixed axes, and a spherical crystal factor Q( r, 2 ), where is the linear absorption coefficient and r the effective radius of the crystal: Icorrected ¼ Iraw SðnÞPðu; v;wÞQð r; 2 Þ: ð1Þ Similar approximations were used by Kopfmann & Huber (1968), North et al. (1968) and Huber & Kopfmann (1969) and in many subsequent papers and programs....

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Journal ArticleDOI
TL;DR: The crystal structure of human erythrocytic ubiquitin has been refined at 1.8 A resolution using a restrained least-squares procedure and features a number of unusual secondary structural features, including a parallel G1 beta-bulge, two reverse Asx turns, and a symmetrical hydrogen-bonding region that involves the two helices and two of the reverse turns.

1,642 citations

Journal ArticleDOI
16 Aug 1979-Nature
TL;DR: It is concluded that X-ray diffraction can provide the spatial distribution of the dynamic features of a protein.
Abstract: X-ray diffraction at four temperatures from 220 to 300 K coupled with crystallographic refinement yields the mean-square displacements and conformational potentials of all 1,261 non-hydrogen atoms of metmyoglobin. The results are interpreted to indicate a condensed core around the haem, semi-liquid regions towards the outside and a possible pathway for ligands. It is concluded that X-ray diffraction can provide the spatial distribution of the dynamic features of a protein.

1,027 citations

Journal ArticleDOI
TL;DR: This study demonstrates that, in horse cytochrome c, the side-chain of Phe82 is positioned in a co-planar fashion next to the heme in a conformation comparable to that found in other cytochromes c, and strongly implicates this internal water molecule as having a functional role in the mechanism of action of cy tochrome c.

992 citations

Journal ArticleDOI
TL;DR: The crystal structure of mammalian calmodulin has been refined at 2.2 A (1 A = 0.1 nm) resolution using a restrained least-squares method and shows a large hydrophobic cleft in each half of the molecule.

989 citations

References
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Journal ArticleDOI

347 citations

ReportDOI
01 Apr 1962
TL;DR: A Fortran program is described for calculating the absorption correction for application to single crystal x ray or neutron intensity measurements and is available in the form of symbolic punched cards.
Abstract: A Fortran program is described for calculating the absorption correction for application to single crystal x ray or neutron intensity measurements. The program is available in the form of symbolic punched cards. InstrucPions are included. (J.R.D.)

24 citations