3txh › Citations

Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals.

Figure 1
Figure 2
Figure 3
Tanley SW, Schreurs AM, Helliwell JR, Kroon-Batenburg LM
OpenAccess logo J Appl Crystallogr 46 108-119 (2013)
Related entries: 3txb, 3txd, 3txe, 3txf, 3txg, 3txi, 3txj, 3txk

Cited: 14 times
EuropePMC logo PMID: 23396873

Abstract

The International Union of Crystallography has for many years been advocating archiving of raw data to accompany structural papers. Recently, it initiated the formation of the Diffraction Data Deposition Working Group with the aim of developing standards for the representation of these data. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. A recent study on the effects of dimethyl sulfoxide on the binding of cisplatin and carboplatin to histidine in 11 different lysozyme crystals from two diffractometers led to an investigation of the possible effects of the equipment and X-ray diffraction data processing software on the calculated occupancies and B factors of the bound Pt compounds. 35.3 Gb of data were transferred from Manchester to Utrecht to be processed with EVAL. A systematic comparison shows that the largest differences in the occupancies and B factors of the bound Pt compounds are due to the software, but the equipment also has a noticeable effect. A detailed description of and discussion on the availability of metadata is given. By making these raw diffraction data sets available via a local depository, it is possible for the diffraction community to make their own evaluation as they may wish.

Articles - 3txh mentioned but not cited (3)

  1. Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin. Shabalin I, Dauter Z, Jaskolski M, Minor W, Wlodawer A. Acta Crystallogr D Biol Crystallogr 71 1965-1979 (2015)
  2. Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals. Tanley SW, Schreurs AM, Helliwell JR, Kroon-Batenburg LM. J Appl Crystallogr 46 108-119 (2013)
  3. Experiences with archived raw diffraction images data: capturing cisplatin after chemical conversion of carboplatin in high salt conditions for a protein crystal. Tanley SW, Diederichs K, Kroon-Batenburg LM, Schreurs AM, Helliwell JR. J Synchrotron Radiat 20 880-883 (2013)


Reviews citing this publication (1)

  1. Error estimates in atom coordinates and B factors in macromolecular crystallography. Helliwell JR. Curr Res Struct Biol 6 100111 (2023)

Articles citing this publication (10)

  1. A public database of macromolecular diffraction experiments. Grabowski M, Langner KM, Cymborowski M, Porebski PJ, Sroka P, Zheng H, Cooper DR, Zimmerman MD, Elsliger MA, Burley SK, Minor W. Acta Crystallogr D Struct Biol 72 1181-1193 (2016)
  2. The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years. Grabowski M, Cymborowski M, Porebski PJ, Osinski T, Shabalin IG, Cooper DR, Minor W. Struct Dyn 6 064301 (2019)
  3. Protein Recognition of Gold-Based Drugs: 3D Structure of the Complex Formed When Lysozyme Reacts with Aubipy(c.). Messori L, Cinellu MA, Merlino A. ACS Med Chem Lett 5 1110-1113 (2014)
  4. An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography. Butryn A, Simon PS, Aller P, Hinchliffe P, Massad RN, Leen G, Tooke CL, Bogacz I, Kim IS, Bhowmick A, Brewster AS, Devenish NE, Brem J, Kamps JJAG, Lang PA, Rabe P, Axford D, Beale JH, Davy B, Ebrahim A, Orlans J, Storm SLS, Zhou T, Owada S, Tanaka R, Tono K, Evans G, Owen RL, Houle FA, Sauter NK, Schofield CJ, Spencer J, Yachandra VK, Yano J, Kern JF, Orville AM. Nat Commun 12 4461 (2021)
  5. Effect of temperature on the interaction of cisplatin with the model protein hen egg white lysozyme. Ferraro G, Pica A, Russo Krauss I, Pane F, Amoresano A, Merlino A. J Biol Inorg Chem 21 433-442 (2016)
  6. Crystals of Na(+)/K(+)-ATPase with bound cisplatin. Huliciak M, Reinhard L, Laursen M, Fedosova N, Nissen P, Kubala M. Biochem Pharmacol 92 494-498 (2014)
  7. FACT and FAIR with Big Data allows objectivity in science: The view of crystallography. Helliwell JR. Struct Dyn 6 054306 (2019)
  8. Structural evidences for a secondary gold binding site in the hydrophobic box of lysozyme. Ferraro G, Massai L, Messori L, Cinellu MA, Merlino A. Biometals 28 745-754 (2015)
  9. Raw diffraction data are our ground truth from which all subsequent workflows develop. Helliwell JR. Acta Crystallogr D Struct Biol 78 683-689 (2022)
  10. Making your raw data available to the macromolecular crystallography community. Kroon-Batenburg LMJ. Acta Crystallogr F Struct Biol Commun 79 267-273 (2023)


Quick links