International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 11.2, p. 212   | 1 | 2 |

Section 11.2.2. Prerequisites for accurate integration

A. G. W. Lesliea*

aMRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England
Correspondence e-mail: andrew@mrc-lmb.cam.ac.uk

11.2.2. Prerequisites for accurate integration

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11.2.2.1. Crystal parameters

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Only the integration procedure itself will be described in detail in this article. However, in order to obtain the highest quality data possible from a given set of images, there are a number of parameters that need to be determined in advance of, or during, the integration. The most important of these are the unit-cell parameters , which should be determined to an accuracy of a few parts in a thousand (or better). Post-refinement procedures (Winkler et al., 1979[link]; Rossmann et al., 1979[link]), which make use of the estimated ϕ centroids of observed spots rather than their detector coordinates, generally provide more accurate estimates than methods based on the spot positions. This is because spot positions are affected by residual spatial distortions (after applying appropriate corrections) and the cell parameters are correlated with the crystal-to-detector distance, which is not always accurately known. For either method, it is necessary to include data from widely separated regions of reciprocal space (ideally ϕ values 90° apart) in order to determine all unit-cell parameters accurately. This is particularly important for lower-symmetry space groups.

The crystal orientation also needs to be known to an accuracy that corresponds to a few per cent of the reflection width. For crystals with low mosaicity (e.g. 0.1°) this corresponds to a hundredth of a degree or better. Fortunately, it is a feature of post refinement that the error in determining the orientation is typically a few per cent of the reflection width, and so this condition can generally be met. It is important to allow for movement of the crystal by continuously updating the crystal orientation during integration. This is even true when using cryo-cooled crystals, as the magnetic couplings that attach the pin (holding the crystal) to the goniometer head are not strong enough to prevent small movements, particularly with the high angular rotation rates employed on intense synchrotron beamlines. Non-orthogonality of the incident X-ray beam and the rotation axis (if not allowed for) or an off-centre crystal will also give rise to apparent changes in crystal orientation with spindle rotation.

The crystal mosaicity can be estimated by visual inspection and refined by post refinement. Refined values are quite reliable when the mosaic spread is less than about 0.5°, but become more dependent on the rocking-curve model for the high mosaicities that are often associated with frozen crystals. The presence of diffuse scatter, which appears as haloes around the Bragg diffraction spots, presents further difficulties in determining the correct mosaic spread. When processing coarse-sliced images it is preferable to overestimate the mosaic spread slightly (rather than underestimate it). This will result in an increase in random errors (by adding in the X-ray background from an image on which the spot is not actually present), whereas using too small a value can give systematic errors (by underestimating the number of images on which the spot lies).

11.2.2.2. Detector parameters

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Detector calibration is essential for high data quality. Both the spatial distortion and the non-uniformity of response of the detector must be accurately known, and it is equally important that these corrections are stable over the timescale of the experiment (and preferably for much longer).

Finally, the crystal-to-detector distance, the detector orientation and the direct-beam position must be refined and continuously updated during integration, using observed spot positions. The crystal-to-detector distance can vary during data collection if the crystal is not exactly centred on the rotation axis, and the direct-beam position can move after a beam refill at a synchrotron. For image-plate detectors with two (or more) plates, the direct-beam position and detector distance often differ slightly for different plates.

With appropriate care, it is normally possible to predict reflection positions on the detector to an accuracy of 20–30 µm, or a fraction of the pixel size, particularly for highly collimated X-ray beams available at synchrotron sources. This level of accuracy is necessary to minimize possible systematic errors, particularly in the case of profile fitting.

References

Rossmann, M. G., Leslie, A. G. W., Abdel-Meguid, S. S. & Tsukihara, T. (1979). Processing and post-refinement of oscillation camera data. J. Appl. Cryst. 12, 570–581.
Winkler, F. K., Schutt, C. E. & Harrison, S. C. (1979). The oscillation method for crystals with very large unit cells. Acta Cryst. A35, 901–911.








































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