Abstract
Diffraction anisotropy is characterized by variation in diffraction quality with reciprocal lattice direction. In the example presented here, diffraction extended to 2.1 Å resolution along a* and c* directions but only to 3.0 Å along the b* direction. Severe anisotropy such as this is often associated with lack of detail in electron density maps, stalled model improvement, and poor refinement statistics. Published methods for overcoming these difficulties have been combined and implemented in the diffraction anisotropy server. Specifically, the server offers information to diagnose the degree of anisotropy, and then applies ellipsoidal resolution boundaries, anisotropic scaling, and B-factor sharpening to the data set to compensate for the deleterious effects of diffraction anisotropy. Here, I offer advice on implementing these methods to facilitate refinement of macromolecular structures in cases of severely anisotropic data.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Strong M, Sawaya MR, Wang S et al (2006) Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc Natl Acad Sci USA 103:8060–8065
Karplus PA, Diederichs K (2012) Linking crystallographic model and data quality. Science 336:1030–1033
Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. In: Carter CW Jr, Sweet RM (eds) Methods in enzymology: macromolecular crystallography, part A, vol 276. Academic, New York, pp 307–326
Kabsch W (2010) XDS. Acta Crystallogr D 66:125–132
Winn MD, Ballard CC, Cowtan KD et al (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D 67:235–242
McCoy AJ, Grosse-Kunstleve RW, Adams PD et al (2007) Phaser crystallographic software. J Appl Crystallogr 40:658–674
Emsley P, Lohkamp B, Scott WG et al (2010) Features and development of Coot. Acta Crystallogr D 66:486–501
Lee M, Maher MJ, Guss JM (2007) Structure of the T109S mutant of Escherichia coli dihydroorotase complexed with the inhibitor 5-fluoroorotate: catalytic activity is reflected by the crystal form. Acta Crystallogr F 63:154–161
Suits MD, Sperandeo P, Dehò G et al (2008) Novel structure of the conserved Gram-negative lipopolysaccharide transport protein LptA and mutagenesis analysis. J Mol Biol 380:476–488
de Chiara C, Rees M, Menon RP et al (2013) Self-assembly and conformational heterogeneity of the AXH domain of ataxin-1: an unusual example of a chameleon fold. Biophys J 104:1304–1313
Acknowledgment
I am grateful to Duilio Cascio for helpful comments regarding this manuscript and the diffraction anisotropy server.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Sawaya, M.R. (2014). Methods to Refine Macromolecular Structures in Cases of Severe Diffraction Anisotropy. In: Chen, Y. (eds) Structural Genomics. Methods in Molecular Biology, vol 1091. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-691-7_15
Download citation
DOI: https://doi.org/10.1007/978-1-62703-691-7_15
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-690-0
Online ISBN: 978-1-62703-691-7
eBook Packages: Springer Protocols