The application of hierarchical cluster analysis to the selection of isomorphous crystals.

It is generally assumed that the quality of X-ray diffraction data can be improved by merging data sets from several crystals. However, this effect is only valid if the data sets used are from crystals that are structurally identical. It is found that frozen macromolecular crystals very often have relatively low structure identity (and are therefore not isomorphous); thus, to obtain a real gain from multi-crystal data sets one needs to make an appropriate selection of structurally similar crystals. The application of hierarchical cluster analysis, based on the matrix of the correlation coefficient between scaled intensities, is proposed for the identification of isomorphous data sets. Multi-crystal single-wavelength anomalous dispersion data sets from four different protein molecules have been probed to test the applicability of this method. The use of hierarchical cluster analysis permitted the selection of batches of data sets which when merged together significantly improved the crystallographic indicators of the merged data and allowed solution of the structure.

[1]  Pedro M. Valero-Mora,et al.  ggplot2: Elegant Graphics for Data Analysis , 2010 .

[2]  Elspeth F. Garman,et al.  Radiation damage in macromolecular crystallography: what is it and why should we care? , 2010, Acta crystallographica. Section D, Biological crystallography.

[3]  A. N. Popov,et al.  Optimization of data collection taking radiation damage into account , 2010, Acta crystallographica. Section D, Biological crystallography.

[4]  A. Urzhumtsev,et al.  Cluster analysis for phasing with molecular replacement: a feasibility study , 2009, Acta crystallographica. Section D, Biological crystallography.

[5]  D. Hofmann,et al.  Cluster analysis and completeness of crystal structure generation , 2009 .

[6]  Elspeth F Garman,et al.  Absorbed dose calculations for macromolecular crystals: improvements to RADDOSE. , 2009, Journal of synchrotron radiation.

[7]  J. Helliwell,et al.  The interdependence of wavelength, redundancy and dose in sulfur SAD experiments. , 2008, Acta crystallographica. Section D, Biological crystallography.

[8]  Andrea Schmidt,et al.  On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths. , 2007, Acta crystallographica. Section D, Biological crystallography.

[9]  R. Ravelli,et al.  Radiation damage in macromolecular cryocrystallography. , 2006, Current opinion in structural biology.

[10]  Didier Nurizzo,et al.  The ID23-1 structural biology beamline at the ESRF. , 2006, Journal of synchrotron radiation.

[11]  Raimond B G Ravelli,et al.  Improving radiation-damage substructures for RIP. , 2005, Acta crystallographica. Section D, Biological crystallography.

[12]  Manfred S Weiss,et al.  On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength. , 2005, Acta crystallographica. Section D, Biological crystallography.

[13]  Thomas R. Schneider,et al.  HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs , 2004 .

[14]  B. Halle Biomolecular cryocrystallography: structural changes during flash-cooling. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Wei Dong,et al.  High-throughput powder diffraction. II. Applications of clustering methods and multivariate data analysis , 2004 .

[16]  George M Sheldrick,et al.  Substructure solution with SHELXD. , 2002, Acta crystallographica. Section D, Biological crystallography.

[17]  B. Matthews,et al.  Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions. , 2001, Journal of molecular biology.

[18]  Wolfgang Kabsch,et al.  Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants , 1993 .

[19]  W. Hendrickson,et al.  Multi-crystal anomalous diffraction for low-resolution macromolecular phasing. , 2011, Acta crystallographica. Section D, Biological crystallography.

[20]  G. Sheldrick A short history of SHELX. , 2008, Acta crystallographica. Section A, Foundations of crystallography.

[21]  R. Irvin,et al.  Pros and cons of cryocrystallography: should we also collect a room-temperature data set? , 2005, Acta crystallographica. Section D, Biological crystallography.

[22]  Ram Seshadri Crystal structures , 2004 .