State-of-the-Art
Crystallographic Refereeing
General Message:
Deposition of Reflection Data should be
Obligitary
Why? Three examples
Ton Spek,
Utrecht University, The Netherlands
ACA-Honolulu - July 23, 2013
The Purpose of Refereeing an X-RAY
Study is to Check:
• Is the supplied information complete for a meaningful
structure report and evaluation?
• Is the data quality adequate for the conclusions drawn?
• Are proper data collection and structure analysis techniques
used?
• Is the structure correct?
• Is the interpretation of the result correct?
• Are there additional observations of interest but missed by
the authors?
• Is this a duplication with no added value or even a fraud?
Data Needed for Proper Refereeing
• The Refinement Model (Coordinates, con/restraints
etc.).
• The reflection data on which the Model is based.
• For Acta Cryst. this implies the deposition of a
parameter ‘CIF’ and an Fobs/Fcalc ‘FCF’.
• The new SHELXL2013 offers an option for the inclusion
of both types of information in a single (CIF) file.
• This allows for the creation of a proper automated
validation report and data archival.
• It also provides an option for additional independent
calculations where relevant.
IUCr CheckCIF Validation
• The IUCr has set up an elaborate validation system
for structures published in its own Acta Cryst.
Journals.
• Most chemical journals now also require authors to
deposit a CIF and to supply a validation report for use
by the referees but do not require the deposition of
the reflection data.
• The problem is that authors and referees still have to
understand the implication of ALERT issues.
• Even with Acta Cryst. the above sometimes fails as
shown in the next example (Paper withdrawn now).
Acta Cryst. (2011). E67, m576-m577
Is this structure correct ?
[Co4Cl4(C3H6S)4]
R1 = 0.041
wR2 = 0.125
Co  Zn
C3  N1
C6  N2
R1 = 0.028
wR2 = 0.072
Identical to:
Inorg. Chem.
(2006) 45, 8318
Correction
proved with
reflection data
Problem Example from Chemical Journal
Biswas et al.
Eur. J. Inorg. Chem.
(2012) 4479-4485.
R1 = 0.08, wR2 = 0.30
Space Group C2/c
Fe-Complex on 2-axis
NO3 Anion in general
pos. Population = 0.5 !?
Problematic Structure (Biswas et al.)
• Problem: NO3- in general position disordered over
two symmetry related sites sounds strange
(precedents ?).
• Significant residual density peaks up to 2.5 e/Å3 but
explained away as ‘With no chemical significance’
• Reflection data would be needed for a detailed
analysis of the issue but only a CIF was deposited.
• Martin Lutz et al. resynthesised the compound
following the Biswas et al. protocol with a surprising
result (Eur. J. Inorg. Chem. (2013) 2467-2469)
• C2/c  Cc and NO3  NO3 + Acetic acid + H2O
Biswas et al.
Lutz et al.
C2/c – Biswas et al. - VOIDS
Cc – Lutz et al.
Follow-Up
- Biswas et al. maintain their rebuttal
[Eur. J. Inorg. Chem. (2013) 2470]
with their interpretation. 
- Referee conclusion (with no access
to the reflection data): Two different structures !!!
- I obtained the reflection data from one of the co-authors
- A SQUEEZE test run on the Biswas et al. data, with the
NO3- removed, recovered 279 electrons from the voids
left where only 128 were expected for an NO3- model.
- Run on Lutz et al. data, with NO3 and solvents removed,
recovered 285 electrons of the expected 296. Conclusion ?
Widely Cited Nature paper in the
News
Nature (2013) 495, 461
Did a Crystallographic Referee have
a serious look at the data ?
• The deposited CIFs bring up multiple validation
issues in need of further and detailed analysis.
• Important information is lacking to justify the use of
the SQUEEZE technique in this MOF context. Its use
is probably not valid in this application.
• Of particular interest are the details of the reported
structure determination of miyakosyne A with a
population of 50%.
• No reflection data have been deposited to allow for
an independent analysis of the structures.
From Nature
Paper
Major Important Error Types
•
•
•
•
•
•
Wrong atom type assignments (e.g. Cu for Zn)
Problems with hydrogen atoms (too few or too many etc.)
Missed twinning
Missed disordered solvent
Artificial ‘disorder’ due to wrong structure analysis
Wrong symmetry
• All the above may lead to one strong ALERT but more often it
leads to multiple weaker ALERTS that in combination would
indicate a strong ALERT.
• We usully need the reflection data to sort out those ALERTS
Plea for the deposition of both the
‘CIF’ and the reflection data
• A minimum would be the parameter CIF and the
Fo/Fc data from the final refinement (FCF).
• Better: Embed the refinement details and the
observed data in the CIF. The IUCr/Acta Cryst.
provides for that purpose the data names
_iucr_refine_instructions_details and
_iucr_refine_reflections_details
• The new SHELXL2013 does this by embedding
automatically (with data names starting with
_shelx_) and adds checksums.
Final Comments
• CheckCIF provides a list of issues that need to be
addressed, either with a correction or giving an
acceptable explanation.
• ALERTS come in levels A, B & C and report possible error,
missing data or quality issues. G-ALERTS are generally
informative and not necessarily errors but still need to
be looked at seriously.
• A & B ALERTS should never automatically lead to the
rejection of a paper but should be investigated by a
professional crystallographer.
• Everything unusual marked as ‘new’, ‘unexpected’ etc. in
a paper should be approached with healthy mistrust.
For the Discussion
• Do we need different validation criteria for papers in
crystallographic journals such as Acta Cryst. and papers
published in chemical journals ?
• Should deposition of the reflection data be required by
all journals (Standard now in the macromolecular
crystallography community) ?
• Should the validation report along with (where relevant)
the authors’ comments be published as supplementary
material ?
Thanks
to
George Sheldrick for the major 2013 update
of SHELXL
and
my former coworker Martin Lutz and
many others for useful comments and
suggestions