checkCIF validation ALERTS: what they mean and how to respond

Abstract

Authors of a paper that includes a new crystal-structure determination are expected to not only report the structural results of interest and their interpretation, but are also expected to archive in computer-readable CIF format the experimental data on which the crystal-structure analysis is based. Additionally, an IUCr/checkCIF validation report will be required for the review of a submitted paper. Such a validation report, automatically created from the deposited CIF file, lists as ALERTS not only potential errors or unusual findings, but also suggestions for improvement along with interesting information on the structure at hand. Major ALERTS for issues are expected to have been acted on already before the submission for publication or discussed in the associated paper and/or commented on in the CIF file. In addition, referees, readers and users of the data should be able to make their own judgment and interpretation of the underlying experimental data or perform their own calculations with the archived data. All the above is consistent with the FAIR (findable, accessible, interoperable, and reusable) initiative [Helliwell (2019). Struct. Dyn. 6, 05430]. Validation can also be helpful for less experienced authors in pointing to and avoiding of crystal-structure determination and interpretation pitfalls. The IUCr web-based checkCIF server provides such a validation report, based on data uploaded in CIF format. Alternatively, a locally installable checkCIF version is available to be used iteratively during the structure-determination process. ALERTS come mostly as short single-line messages. There is also a short explanation of the ALERTS available through the IUCr web server or with the locally installed PLATON/checkCIF version. This paper provides additional background information on the checkCIF procedure and additional details for a number of ALERTS along with options for how to act on them.

A novel three-dimensional zinc(II) coordination polymer based on 3,3′-{[1,3-phenylenebis(methylene)]bis(oxy)}dibenzoic acid and 1,4-bis(pyridin-4-yl)benzene: synthesis, crystal structure and photocatalytic properties

“…3(a), the whole framework contains 1D channels along the c direction, which are composed of intertwined [Zn 2 (PMBD) 2 ] n chains. The voids are filled with free DPB molecules, and the free space occupies 6.9% of the total The coordination environment of (a) the dinuclear {Zn 2 } cluster and (b) the organic ligand PMBD 2À of CP 1. crystal volume (calculated by PLATON; Spek, 2020). It should be pointed out that the solvent-accessible volume would reach 31.6% if all extra-framework species are removed in the structure.…”

Synthesis, experimental andin silicostudies ofN-fluorenylmethoxycarbonyl-O-tert-butyl-N-methyltyrosine, coupled with CSD data: a survey of interactions in the crystal structures of Fmoc–amino acids

“…2.3. Crystallization, single-crystal X-ray structure determination and refinement Good-quality plate-shaped single crystals suitable for X-ray diffraction (SC-XRD) analysis were grown by vapour diffu- Computer programs: XSCANS (Siemens, 1996), SHELXT (Sheldrick, 2015a), SHELXL2014 (Sheldrick, 2015b), Mercury (Macrae et al, 2020) and PLATON (Spek, 2020). sion over a period of a few weeks.…”

“…The Kitaigorodsky Packing Index (KPI) (Kitaigorodskii, 1961(Kitaigorodskii, , 1973 was calculated with the 'calc void' routine as implemented in PLATON (Spek, 2020). Results revealed that the percentages of filled space are 66.7 and 70.1% in (1) and OGIXOT, respectively, and indicate a tight packing of the molecules in the crystal.…”

Influence of fluorine substitution on the molecular conformation of 3′-deoxy-3′-fluoro-5-methyluridine

“…S1-S4 for NMR spectra]. Compound (1) Computer programs: APEX2 (Bruker, 2006), SAINT (Bruker, 2006), SHELXS97 (Sheldrick, 2008), SHELXL2013 (Sheldrick, 2015), ORTEP-3 (Farrugia, 2012), Mercury (Macrae et al, 2020), SHELXTL (Bruker, 2006), PLATON (Spek, 2020) and publCIF (Westrip, 2010).…”

“…Data collection: APEX2 (Bruker, 2006); cell refinement: SAINT (Bruker, 2006); data reduction: SAINT (Bruker, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015); molecular graphics: ORTEP-3 (Farrugia, 2012) and Mercury (Macrae et al, 2020); software used to prepare material for publication: SHELXTL (Bruker, 2006), PLATON (Spek, 2020) and publCIF (Westrip, 2010).…”