The Science is in the Data

Overview

Journal IUCrJ

Date 2017 Nov 11

PMID 29123672

Citations 16

Authors

John R Helliwell

BrIan McMahon

J Mitchell Guss

Loes M J Kroon-Batenburg

Affiliations

Soon will be listed here.

Abstract

Understanding published research results should be through one's own eyes and include the opportunity to work with raw diffraction data to check the various decisions made in the analyses by the original authors. Today, preserving raw diffraction data is technically and organizationally viable at a growing number of data archives, both centralized and distributed, which are empowered to register data sets and obtain a preservation descriptor, typically a 'digital object identifier'. This introduces an important role of preserving raw data, namely understanding where we fail in or could improve our analyses. Individual science area case studies in crystallography are provided.

Citing Articles

Raw diffraction data and reproducibility.

Kroon-Batenburg L, Lightfoot M, Johnson N, Helliwell J Struct Dyn. 2024; 11(1):011301.

PMID: 38361661 PMC: 10869167. DOI: 10.1063/4.0000232.

Making your raw data available to the macromolecular crystallography community.

Kroon-Batenburg L Acta Crystallogr F Struct Biol Commun. 2023; 79(Pt 10):267-273.

PMID: 37815476 PMC: 10565795. DOI: 10.1107/S2053230X23007987.

The four Rs and crystal structure analysis: reliability, reproducibility, replicability and reusability.

Helliwell J, Massera C J Appl Crystallogr. 2022; 55(Pt 5):1351-1358.

PMID: 36249510 PMC: 9533758. DOI: 10.1107/S1600576722007208.

Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography.

Helliwell J Methods Mol Biol. 2022; 2449:235-261.

PMID: 35507266 DOI: 10.1007/978-1-0716-2095-3_10.

Making the collective knowledge of chemistry open and machine actionable.

Jablonka K, Patiny L, Smit B Nat Chem. 2022; 14(4):365-376.

PMID: 35379967 DOI: 10.1038/s41557-022-00910-7.

References

Kroon-Batenburg L, Helliwell J, McMahon B, Terwilliger T . Raw diffraction data preservation and reuse: overview, update on practicalities and metadata requirements. IUCrJ. 2017; 4(Pt 1):87-99. PMC: 5331468. DOI: 10.1107/S2052252516018315. View

Grabowski M, Langner K, Cymborowski M, Porebski P, Sroka P, Zheng H . A public database of macromolecular diffraction experiments. Acta Crystallogr D Struct Biol. 2016; 72(Pt 11):1181-1193. PMC: 5108346. DOI: 10.1107/S2059798316014716. View

Meng Z, Lou Z, Liu Z, Li M, Zhao X, Bartlam M . Crystal structure of human pyrroline-5-carboxylate reductase. J Mol Biol. 2006; 359(5):1364-77. DOI: 10.1016/j.jmb.2006.04.053. View

Pozharski E, Weichenberger C, Rupp B . Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures. Acta Crystallogr D Biol Crystallogr. 2013; 69(Pt 2):150-67. DOI: 10.1107/S0907444912044423. View

Joosten R, Long F, Murshudov G, Perrakis A . The PDB_REDO server for macromolecular structure model optimization. IUCrJ. 2014; 1(Pt 4):213-20. PMC: 4107921. DOI: 10.1107/S2052252514009324. View

Oldham M, Brash A, Newcomer M . Insights from the X-ray crystal structure of coral 8R-lipoxygenase: calcium activation via a C2-like domain and a structural basis of product chirality. J Biol Chem. 2005; 280(47):39545-52. DOI: 10.1074/jbc.M506675200. View

Weiss M, Diederichs K, Read R, Panjikar S, Van Duyne G, Matera A . A critical examination of the recently reported crystal structures of the human SMN protein. Hum Mol Genet. 2016; 25(21):4717–4725. PMC: 5418738. DOI: 10.1093/hmg/ddw298. View

Guss J, McMahon B . How to make deposition of images a reality. Acta Crystallogr D Biol Crystallogr. 2014; 70(Pt 10):2520-32. PMC: 4188000. DOI: 10.1107/S1399004714005185. View

Terwilliger T, Bricogne G . Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data. Acta Crystallogr D Biol Crystallogr. 2014; 70(Pt 10):2533-43. PMC: 4188001. DOI: 10.1107/S1399004714017040. View

10.

Minor W, Dauter Z, Helliwell J, Jaskolski M, Wlodawer A . Safeguarding Structural Data Repositories against Bad Apples. Structure. 2016; 24(2):216-20. PMC: 4743038. DOI: 10.1016/j.str.2015.12.010. View

11.

Weichenberger C, Pozharski E, Rupp B . Visualizing ligand molecules in Twilight electron density. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013; 69(Pt 2):195-200. PMC: 3564628. DOI: 10.1107/S1744309112044387. View

12.

Seng C, Magee C, Young P, Lorson C, Allen J . The SMN structure reveals its crucial role in snRNP assembly. Hum Mol Genet. 2015; 24(8):2138-46. DOI: 10.1093/hmg/ddu734. View

13.

Rupp B, Wlodawer A, Minor W, Helliwell J, Jaskolski M . Correcting the record of structural publications requires joint effort of the community and journal editors. FEBS J. 2016; 283(24):4452-4457. PMC: 5124416. DOI: 10.1111/febs.13765. View

14.

Rhys N, Wang M, Jowitt T, Helliwell J, Grossmann J, Baldock C . Deriving the ultrastructure of α-crustacyanin using lower-resolution structural and biophysical methods. J Synchrotron Radiat. 2010; 18(1):79-83. PMC: 3004261. DOI: 10.1107/S0909049510034977. View

15.

Shabalin I, Dauter Z, Jaskolski M, Minor W, Wlodawer A . Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin. Acta Crystallogr D Biol Crystallogr. 2015; 71(Pt 9):1965-79. PMC: 4556316. DOI: 10.1107/S139900471500629X. View

16.

Tanley S, Schreurs A, Helliwell J, Kroon-Batenburg L . Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals. J Appl Crystallogr. 2013; 46(Pt 1):108-119. PMC: 3547227. DOI: 10.1107/S0021889812044172. View

17.

Zadrozny J, Xiao D, Atanasov M, Long G, Grandjean F, Neese F . Magnetic blocking in a linear iron(I) complex. Nat Chem. 2013; 5(7):577-81. DOI: 10.1038/nchem.1630. View

18.

Tanley S, Diederichs K, Kroon-Batenburg L, Levy C, Schreurs A, Helliwell J . Carboplatin binding to histidine. Acta Crystallogr F Struct Biol Commun. 2014; 70(Pt 9):1135-42. PMC: 4157408. DOI: 10.1107/S2053230X14016161. View

19.

Meyer P, Socias S, Key J, Ransey E, Tjon E, Buschiazzo A . Data publication with the structural biology data grid supports live analysis. Nat Commun. 2016; 7:10882. PMC: 4786681. DOI: 10.1038/ncomms10882. View

20.

Marsh R, Kapon M, Hu S, Herbstein F . Some 60 new space-group corrections. Acta Crystallogr B. 2002; 58(Pt 1):62-77. DOI: 10.1107/s0108768101017128. View