Abstract
X-ray crystallography offers precious and striking knowledge on biomolecular architectures. Although safeguards do exist to guarantee the accuracy of the structures deposited in databases, they are not always applied, leading to the spread of inaccurate data. The importance of validation reports in the publication process is emphasized.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Brown EN, Ramaswamy S (2007) Quality of protein crystal structures. Acta Cryst D 63:941–950
Read RJ, Adams PD, Arendall WB 3rd, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lutteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH (2011) A new generation of crystallographic validation tools for the protein data bank. Structure 19:1395–1412
Chou FC, Sripakdeevong P, Dibrov SM, Hermann T, Das R (2013) Correcting pervasive errors in RNA crystallography through enumerative structure prediction. Nat Methods 10:74–76
Wlodawer A, Minor W, Dauter Z, Jaskolski M (2013) Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination. FEBS J 280:5705–5736
Brändén C-I, Jones TA (1990) Between objectivity and subjectivity. Nature 343:687–689
Dauter Z, Wlodawer A, Minor W, Jaskolski M, Rupp B (2014) Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining. IUCrJ 1:179–193
Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB 3rd, Snoeyink J, Richardson JS, Richardson DC (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375–W383
Sundaralingam M, Jensen LH (1965) Stereochemistry of nucleic acid constituents. I. Refinement of the structure of cytidylic acid b. J Mol Biol 13:914–929
Kennard O, Allen FH, Brice MD, Hummelink TWA, Motherwell WDS, Roidgers JR, Watson DG (1977) Computer based systems for the retrieval of data:crystallographyt. Pure Appl Chem 49:1807–1816
Bernstein FC, Koetzle TF, Williams GJ, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977) The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 112:535–542
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer Science+Business Media New York
About this protocol
Cite this protocol
Westhof, E. (2016). Perspectives and Pitfalls in Nucleic Acids Crystallography. In: Ennifar, E. (eds) Nucleic Acid Crystallography. Methods in Molecular Biology, vol 1320. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2763-0_1
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2763-0_1
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2762-3
Online ISBN: 978-1-4939-2763-0
eBook Packages: Springer Protocols