This proposal is in response to the recent, dramatic expansion in the fields of structural biology. Progress in genetics and biochemistry created a need for precise stereochemical understanding of large numbers of macromolecules. Progress in X-ray instrumentation and computing hardware makes this possible. Based on our experience in developing the widely used macromolecular X-ray crystallography HKL data reduction package (Denzo, Scalepack, XdisplayF) we propose to further develop this area.
The specific aims of this proposal are: 1) to develop data reduction methods for imperfect crystals - highly mosaic or twinned. it will be possible to index more than one diffraction pattern in one detector image, calculate overlap between diffraction patterns and correct for Bragg peak tails of reflection intruding upon each other. 2) to expand the Multiwavelength Anomalous Dispersion (MAD) method to cases where the signal-to-error ratio is currently insufficient for structure determination. This will be accomplished by calibrating and correcting for instrument response factors that now limit the MAD method to well diffracting crystals with relatively high anomalous diffraction signal. 3) to provide optimal data collection strategy by simulating in advance of data collection the expected reciprocal space coverage and detector resolution as a function of possible settings - data collection angles and crystal-to-detector distance. 4) to provide real-time feedback by reducing data on-line and calculating synthetic statistics. This is of particular significance to users of synchrotron facilities who need to wait for months to repeat their experiments. 5) to expand the range of the crystallographic experiments treated optimally in data reduction by deconvolution of partially overlapping reflections and 3-D profile fitting, to develop automatic and interactive editing tools in order to minimize the influence of possible experimental artifacts on the reduced data. 6) to expand methods to visually inspect the process of data collection and data reduction from current direct visualization of raw data to synthetic visual representation of factors affecting data quality - average reflection profiles, de convolution integrals, crystal slippage, detector response function and others. 7) to provide data base style organizational tools for the experimenter to follow the entire crystallographic project. The data base will be used to create unified reports - merging statistics, coverage, decay, slippage etc. Lastly, all of the above developments will be integrated into one efficient, simple to use computer and detector general software package. The resulting software will increase precision and reliability of three-D structures of macromolecules by x-ray crystallography, enable to solve crystal structures too difficult to solve with the present methods, and will speed-up, simplify and reduce the time and effort required of the structure determination process, speeding up understanding of biological systems and structure based drug design.
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| Li, Wenlin; Schaeffer, R Dustin; Otwinowski, Zbyszek et al. (2016) Estimation of Uncertainties in the Global Distance Test (GDT_TS) for CASP Models. PLoS One 11:e0154786 |
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| Bromberg, Raquel; Grishin, Nick V; Otwinowski, Zbyszek (2016) Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer. PLoS Comput Biol 12:e1004985 |
| Lee, Jyh-Yeuan; Kinch, Lisa N; Borek, Dominika M et al. (2016) Crystal structure of the human sterol transporter ABCG5/ABCG8. Nature 533:561-4 |
| Meyer, Peter A; Socias, Stephanie; Key, Jason et al. (2016) Data publication with the structural biology data grid supports live analysis. Nat Commun 7:10882 |
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