Processing incommensurately modulated protein diffraction data with Eval15.
Jason Porta,Jeffrey J. Lovelace,Antoine M. M. Schreurs,Loes M. J. Kroon-Batenburg,Gloria E. O. Borgstahl +4 more
TL;DR: This is the first report of the processing of data from an incommensurately modulated macromolecular crystal using the Eval program suite and can be used as a guide for protein crystallographers when encountering crystal modulations.
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Abstract: Recent challenges in biological X-ray crystallography include the processing of modulated diffraction data. A modulated crystal has lost its three-dimensional translational symmetry but retains long-range order that can be restored by refining a periodic modulation function. The presence of a crystal modulation is indicated by an X-ray diffraction pattern with periodic main reflections flanked by off-lattice satellite reflections. While the periodic main reflections can easily be indexed using three reciprocal-lattice vectors a*, b*, c*, the satellite reflections have a non-integral relationship to the main lattice and require a q vector for indexing. While methods for the processing of diffraction intensities from modulated small-molecule crystals are well developed, they have not been applied in protein crystallography. A recipe is presented here for processing incommensurately modulated data from a macromolecular crystal using the Eval program suite. The diffraction data are from an incommensurately modulated crystal of profilin–actin with single-order satellites parallel to b*. The steps taken in this report can be used as a guide for protein crystallographers when encountering crystal modulations. To our knowledge, this is the first report of the processing of data from an incommensurately modulated macromolecular crystal.
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Citations
Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers
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TL;DR: 11 structures of engineered variants of the E. coli enzyme N-acetyl-neuraminic lyase which, despite twinning and incommensurate modulation, have been successfully indexed, solved and deposited provide an excellent test set for improving and challenging MX data processing programs.
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TL;DR: This review concludes with a projected pathway for solving incommensurately modulated crystals, personal views of future directions and needs of the crystallographic community, and a number of case studies in the literature of lattice order–disorder phenomena and crystallographic modulations.
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References
Processing of X-ray diffraction data collected in oscillation mode
Zbyszek Otwinowski,Wladek Minor +1 more
TL;DR: The methods presented in the chapter have been applied to solve a large variety of problems, from inorganic molecules with 5 A unit cell to rotavirus of 700 A diameters crystallized in 700 × 1000 × 1400 A cell.
33.6K
Numerical recipes
TL;DR: This section discusses a particular type of low-pass filter, well-adapted for data smoothing, and termed variously Savitzky-Golay, least-squares, or DISPO (Digital Smoothing Polynomial) filters.
19K
The integration of macromolecular diffraction data
TL;DR: These equations highlight the importance of the contribution of the X-ray background to the standard error and give an estimate of the improvement which can be achieved by profile fitting.
The finer things in X-ray diffraction data collection
TL;DR: The expectations and consequences of the processing of thick and thin images in terms of spatial overlap, saturated pixels, X-ray background and I/sigma(I) are discussed.