A New Measurement of Crystal Shapes for Absorption Corrections

Izumi, Teruo; Tsuruta, K.; Fujitsuka, A.; Kuchiji, H.; Kurihama, Tadashi

doi:10.1107/s0021889896001628

Cited by 4 publications

(4 citation statements)

References 3 publications

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“…Mounting the crystal on the tip of the micropipette allows the detection of shadow projections via a video system. With the method of back projection, the crystal shape and crystal volume can be easily calculated (Kiefersauer et al, 1996;Izumi et al, 1996). The response of the crystal lattice towards humidity changes can be monitored over time by analysing the crystal extension.…”

Section: Optical Analysis Of the Crystalmentioning

confidence: 99%

A novel free-mounting system for protein crystals: transformation and improvement of diffraction power by accurately controlled humidity changes

et al. 2000

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A novel device for capillary-free mounting of protein crystals is described. A controlled stream of air allows an accurate adjustment of the humidity at the crystal. The crystal is held on the tip of a micropipette. With a video system (CCD camera), the two-dimensional shadow projections of crystals can be recorded for optical analysis. Instead of the micropipette, a standard loop can also be used. Experiments and results for different crystal systems demonstrate the use of this method, also in combination with shock-freezing, to improve crystal order. Working with oxygen-free gases offers the possibility of crystal measurements under anaerobic conditions. Furthermore, the controlled application of arbitrary volatile substances with the gas stream is practicable.

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Section: Optical Analysis Of the Crystalmentioning

confidence: 99%

A novel free-mounting system for protein crystals: transformation and improvement of diffraction power by accurately controlled humidity changes

et al. 2000

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“…Unfortunately, the existing practice of preliminary empirical scaling makes the refinement of sample sizes impossible. Prior to the implementation in diffractometer software of programs developed for reconstructing sample shape from photographs (Izumi et al, 1996;Zhurov, 2005;Leal et al, 2008), our method is most effective. In this paper, it has been shown that empirical absorption correction should be applied only at the very end of calculations, when all other corrections with a physical meaning have already been introduced.…”

Section: Tablementioning

confidence: 99%

New approaches to scaling data measured on a CCD diffractometer

Dudka

2010

J Appl Cryst

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New methods have been developed for scaling the intensities of diffraction reflections measured on a diffractometer with a CCD detector. The algorithm involves cyclic alternation of the refinement of a structure model from experimental data corrected for anisotropic effects with the refinement of anisotropic parameters from initial data for a fixed structure model. The first method consists of refining scale factors for the intensities after they have first been corrected for anisotropic effects of known physical nature (thermal diffuse scattering, absorption, extinction etc.). It has been shown that the majority of the observed biases of intensities are caused by the characteristics of the CCD detector and the technique used for data collection on the diffractometer, rather than by the properties of the sample. The second (alternative) method of fixed scaling has been implemented here. This method does not require refinement of empirical scale factors but uses intensity correction maps obtained by averaging the results derived from several experiments with different crystals. The first map describes the non‐uniformity of the response over the surface area of the detector. The second map accounts for distortions dependent on the setting angles of the goniometer. The methods were checked for data measured on an Oxford Diffraction Xcalibur Sapphire 3 CCD diffractometer. The proposed methods significantly improve the results of the refinement and make it possible to obtain a structure model that is reproduced in repeated investigations of samples of the same compound.

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“…In three dimensions, this leads usually to a volumetric representation in which the object is quantized as a voxel. 2 This type of modelling was implemented for the first time in crystallography by Izumi et al (1996), although the test crystal of V 3 Si had no surrounding support system. In the present work we extend the approach to distinguish between crystal, loop and cryoprotectant components of the mounted sample.…”

Section: Three-dimensional Modelling Of Macromolecular Crystals Cryomentioning

confidence: 99%

Absorption correction based on a three-dimensional model reconstruction from visual images

et al. 2008

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The results are presented of a feasibility study for the application of absorption corrections to macromolecular crystallographic X‐ray diffraction data using a three‐dimensional crystal model generated photographically. The model allows path lengths through the crystal, the solvent and the crystal mount system to be determined. The approach has been tested on the macromolecular crystallography beamline ID23‐1 at the ESRF in Grenoble using a model insulin system with the standard mini diffractometer facilities, which incorporate high‐quality camera systems for sample alignment. Data from the insulin crystal at low incident beam energy (6.0 keV or 2.1 Å) were recorded and processed using this approach. The resulting data are compared against those treated using an empirical method and show significant improvement. The methods described here are of general interest, particularly for long‐wavelength X‐ray work, and may also be applied to account for absorption effects in neutron crystallography.

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A New Measurement of Crystal Shapes for Absorption Corrections

Cited by 4 publications

References 3 publications

A novel free-mounting system for protein crystals: transformation and improvement of diffraction power by accurately controlled humidity changes

A novel free-mounting system for protein crystals: transformation and improvement of diffraction power by accurately controlled humidity changes

New approaches to scaling data measured on a CCD diffractometer

Absorption correction based on a three-dimensional model reconstruction from visual images

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