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 J. Appl. Cryst.
(2003).
36
, 7±13 A. L. Spek
Single-crystal structure validation
7
research papers
 Journal of 
AppliedCrystallography
ISSN 0021-8898Received 27 September 2002Accepted 28 November 2002
#
2003 International Union of CrystallographyPrinted in Great Britain ± all rights reserved
Single-crystal structure validation with the program
PLATON
A. L. Spek
Crystal and Structural Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University,Padualaan 8, 3584 CH Utrecht, The Netherlands. Correspondence e-mail: a.l.spek@chem.uu.nl
The results of a single-crystal structure determination when in CIF format cannow be validated routinely by automatic procedures. In this way, many errors inpublished papers can be avoided. The validation software generates a set of 
evi
detailing issues to be addressed by the experimenter, author, refereeand publication journal. Validation was pioneered by the IUCr journal
ActaCrystallographica Section C 
and is currently standard procedure for structuressubmitted for publication in all IUCr journals. The implementation of validationprocedures by other journals is in progress. This paper describes the concepts of validation and the classes of checks that are carried out by the program
PLATON 
as part of the IUCr
checkCIF 
facility.
PLATON 
validation can be runat any stage of the structure re®nement, independent of the structuredetermination package used, and is recommended for use as a routine toolduring or at least at the completion of every structure determination. Twoexamples are discussed where proper validation procedures could have avoidedthe publication of incorrect structures that had serious consequences for thechemistry involved.
1. Introduction
A single-crystal X-ray study has the unique potential toprovide `solid' knowledge about the three-dimensional struc-ture of molecules and complexes in the crystalline state alongwith their intermolecular interactions. Much of our currentknowledge concerning inorganic and metal-organiccompounds is derived from single-crystal studies. Structuredeterminations that are carried out carefully will generallyprovide incontrovertible results, upon which subsequentresearch can be built. Unfortunately, for various reasons, notall structures that end up in the refereed literature andsubsequently in databases appear to be correct, either beingerroneous only in certain details or containing major errorswhich lead to the derivation of incorrect conclusions. Anexcellent paper by Harlow (1996) discusses many examples.The assignment of the correct space group to a structure is oneof the most common problems, as has been demonstratedmany times by Marsh and others (
e.g.
Marsh & Spek, 2001).Some of the more serious errors include incorrectly assignedatom types and missing or too many hydrogen atoms in astructure, obviously with serious implications for the chem-istry involved. Often, papers include a detailed discussion onan interesting feature of a molecular structure that in hind-sight turns out to be based on an artefact. Parkin (1993)addresses in detail the illusive `bond-stretch isomerism'phenomenon.Technical advances have turned the structure determinationof many crystals of suf®cient quality into a routine procedurein the hands of an experienced crystallographer. Much of thedata collection, structure solution and re®nement steps havebeen automated and often form part of the software packagethat comes with the data-collection instrument. Current CCD(charge-coupled device) detector-based diffractometersystems are capable of producing up to 1000 data sets per year.Computing power, being a serious bottleneck in the past, is nolonger a limiting factor in this ®eld. A modern PC can easilyhandle all the necessary calculations.An important and certainly ®nal part of a structure deter-mination should be the validation of the structural results.Traditionally, this was the responsibility of a professionalcrystallographer and, when submitted for publication, thereferees. The unfortunate current situation is that the numberof structures that are submitted for publication each year isorders of magnitude larger than the number of experiencedcrystallographers and referees knowledgeable in crystal-lography. In addition, referees are often given only limitedaccess to the supporting experimental data or are simplyinformed that all crystallographic details have been deposited.The Cambridge Structural Database (CSD; Allen, 2002)includes many entries with comment records detailingproblems encountered by the data-entry staff during theprocessing of published structures.A recent editorial (Eisenberg, 2002) in
Inorganic Chemistry
addresses the issue of properly `reviewing crystallographicdata'. The International Union of Crystallography (IUCr)identi®ed the general problem a decade ago and created as a®rst step the computer-readable Crystallographic InformationFile (CIF) standard for reporting, exchanging and archiving
 
research papers
8
A. L. Spek
Single-crystal structure validation
J. Appl. Cryst.
(2003).
36
, 7±13
crystal structure data (Hall
et al.
, 1991). Most current softwarepackages can now generate such ®les. Subsequently, a project(
checkCIF 
) was initiated to validate crystal structure datasupplied in CIF format. Currently, the electronic validationprocedures are fully operational.
2. Validation
Single-crystal structure validation addresses three importantissues that can be expressed in the form of the followingquestions:Question 1: is the reported information complete?Question 2: what is the quality of the analysis?Question 3: is the structure correct?The answer to question 1 should be easy since it essentiallyinvolves a checklist of items describing various details of thestructure analysis. Many journals provide in their notes forauthors such a checklist of details to be provided so that otherscan evaluate and repeat the study. The CIF standard offers anadequate mechanism to make this information available forsubsequent electronic processing. The automatic analysis of the data present in the CIF for completeness and internalconsistency is relatively trivial.Judging the quality of a structure determination, question 2,is more dif®cult. It very much depends on factors such ascrystal quality, data collection hardware, expertise of theinvestigator and software used. Nevertheless, various valuescan be calculated that can be compared with some generallyaccepted standards. Examples are resolution and complete-ness of the data set, bond precision (see below), convergenceof the least-squares re®nement and
R
factors. Referees can judge whether the quality of the analysis is sucient tosupport the conclusions drawn from it and meet journalstandards. A journal might choose to publish only thosestructures with the highest attainable quality, which can behigher than needed for the purpose of the study but relevantfor the follow-up research that might build upon it.Question 3 is probably the most important and dif®cult.This is not something to which a computer (program) canprovide a complete answer. What a program can do is toreport on any unusual feature it detects. It is then up to theinvestigator/author to consider the issue, take action if necessary, or otherwise comment convincingly on it. Subse-quently, the referees must decide on the validity of the argu-ments offered.Incorrect structures usually exhibit one or more of threesymptoms: (i) unusual bond distances, (ii) unreasonabledisplacement parameters (ellipsoids) and (iii) impossibleintra- and intermolecular contacts (see below). When unusualstructures are reported, only a high-quality structure mightgive the level of con®dence needed to proclaim that it indeedhas unique features.
3. Validation tests
The IUCr has de®ned and documented a large number of validation tests (http://journals.iucr.org/services/cif/checking/autolist.html) that are carried out for all structures submittedfor publication in IUCr journals. These tests address issuesrelated to questions 1 and 2 detailed above and are readilyavailable through the Web-based IUCr
checkCIF 
facility (http://journals.iucr.org/services/cif/checking/check-form.html). The tests include checks for proper re®nementand absorption correction procedures. The program
 IUCRVAL
(Farrugia, 2000) also incorporates this set of testsand can be implemented locally.The validation function in the program
PLATON 
(Spek,2002) addresses all three questions. The next section of thispaper details the various classes of tests that are implementedin the program.
PLATON 
can also conduct
o
/
c
CIF validation. Issuesaddressed include resolution and completeness of the data set.In particular, missing low-order re¯ection data are reported.However, no details will be presented here.
4. Validation tests implemented in
PLATON
The tests are given a three-digit number,
nxx
, and fall into tengroupings:0
 xx
: this range concerns data completeness, consistency andquality tests.1
 xx
: tests addressing unit-cell and space-group symmetryissues.2
 xx
:issues related to (an)isotropic displacement parameters.3
 xx
: tests and reports on intramolecular issues.4
 xx
: tests and reports on intermolecular issues.5
 xx
: coordination-related issues.6
 xx
: issues related to solvent-accessible voids.7
 xx
: problems with bonds and their associated standarduncertainties.8
 xx
: validation-software problems9
 xx
: problems with the re¯ection data.In the following, a number of the issues addressed will bediscussed in detail.
4.1. Missed symmetry
The assignment of the proper space group to a givenstructure is not always obvious at the beginning of a structuredetermination. Often, a preliminary structure can be obtainedonly in a space group with symmetry that is lower than theactual symmetry. Subsequent analysis should lead to adescription in the correct space group. Unfortunately, thelatter is not always achieved.
 ADDSYM 
, an extended version of the
MISSYM 
algorithm(Le Page, 1987, 1988) is used to search for possibly missedhigher crystallographic symmetry in the reported structure. Atentative, more appropriate, space group is suggested. Inter-estingly, approximations to higher symmetry (pseudo-symmetry) occur frequently. For that reason, missed symmetry
evi
generally require as a follow-up a detailed analysis of the situation `by hand', with access to the primary re¯ectiondata.
 
An attempt to re®ne a centrosymmetric structure in a non-centrosymmetic space group generally results in poorgeometry due to the (near) singularity of the least-squaresnormal matrix. Chemically equivalent bonds may differsigni®cantly and displacement parameters generally makelittle sense in such a case. Proper action includes, apart fromleaving out half of the atoms in the model and the addition of an inversion centre, a shift of the structure to the properorigin. A number of reported cases of missed higher symmetryare due to a failure by the authors to apply such a shift, withthe result that the subsequent re®nement of the centrosym-metric model was reported `unsuccessful'. For a correctedexample of a structure originally published in
P
1 with twocrystallographically independent molecules and an unusual
ORTEP
diagram, see Kahn
et al.
(2000
a
,
b
).The
ADDSYM 
algorithm allows a small percentage of atoms to fail the proposed higher symmetry. Although thisfeature will bring up a number of false
evi
, it will oftencatch cases of missed symmetry in poorly re®ned structures orthose with missing, miss-identi®ed or disordered atoms.
4.2. Voids
Solvent-accessible voids (van der Sluis & Spek, 1990) arereported. Such voids might include disordered solvent thatwent undetected by peak-search algorithms. A commonreason might be that the disorder results in density ridges orfaint plateaus rather than isolated peaks. Except for someframework structures, crystal structures generally collapsewhen they have lost solvent molecules of crystallization.Voids are frequently located at or along symmetry elements.Solvent molecules on those sites are generally highly disor-dered or ®ll one-dimensional channels along three-, four- orsixfold axes.Void
evi
in combination with
evi
on short inter-molecular contacts may point to molecules that are misplacedwith respect to the symmetry elements.
4.3. Displacement ellipsoid tests
A displacement ellipsoid plot (
ORTEP
II; Johnson, 1976) isan excellent validation tool but not suitable as an automatictool. Fortunately, numerical analogues for visual inspection byan expert are available. The Hirshfeld rigid-bond test(Hirshfeld, 1976) can be indicative of many problems with astructural model. The central idea is that the components of the anisotropic displacement parameters along the bond fortwo bonded atoms should have approximately the same value.This will generally not be the case when incorrect atom typesare assigned to density peaks. Carbon atoms might be nitrogenatoms or oxygen,
etc.
Elongated ellipsoids are, in general, indicative of unre-solved disorder. An attempt should be made to develop aproper model to represent the disorder.Many systematic errors (including absorption and wrongwavelength) ®nd their way into the displacement parameters,often giving rise to physically impossible non-positive-de®nitevalues for the main-axis values.
4.4. Bonds and angles
The values of bonds and angles are checked to determinewhether their values fall within expected ranges. Single,double or triple bond types are assigned from the deducedhybridization of the bonded atoms. Bonds that are too short ortoo long may be caused by unresolved disorder. Failure toassign a proper hybridization type to a carbon atom may beindicative of a missing (hydrogen) atom. The average and therange of C bond lengths within a phenyl moiety arecompared with the expected value, 1.395 AÊ. A signi®cantdeviation may indicate incorrect cell dimensions (possiblycalculated with the wrong wavelength), poor diffraction dataor an incorrect re®nement model. When the data quality doesnot support their re®nement, methyl H atoms often behavebadly, giving rise to unrealistic geometry. In addition, thegeometrical data given in the CIFare checked to see that theycorrespond to the values calculated directly from the atomiccoordinate data.A quality indicator called
ond son
is reported andcalculated as the average standard uncertainty on CÐC bonds.
4.5. Intermolecular contacts
Intermolecular contacts can be very informative in indi-cating incorrect structures. Obviously, when atoms approachcloser than the sum of their van der Waals radii there must beeither a missed interaction, such as a hydrogen bond, or theirpositions are in some way in error. Bumping hydrogen atomsmay indicate misplaced hydrogen atoms (
e.g.
two instead of one hydrogen on an
sp
2
carbon) or methyl moieties ®xed in aninappropriate conformation.
4.6. Hydrogen bonds
As a rule, OH moieties are hydrogen bonded to anacceptor. A test is carried out to ®nd out whether this is indeedthe case. Potential H-atom positions lie on a cone. Finding thecorrect position on this cone can be tricky when the differenceelectron-density map does not present a single suitablemaximum.
SHELXL97 
(Sheldrick, 1997) provides an optionto ®nd the optimal position by way of an electron-densitycalculation around a circle. Alternatively, the program
HYDROGEN 
(Nardelli, 1999) may also be used to ®nd anoptimal position based on geometric and energy considera-tions.The analysis of structures containing hydroxy moietiesobtained from the Cambridge Structural Database (CSD;Allen, 2002) gives many examples where hydroxy hydrogenatoms are in the wrong position. For a corrected example, seeKo È rner
et al.
(2000
a
,
b
).
4.7. Connectivity
The CIF is assumed to contain a set of atomic coordinatesthat do not require the application of symmetry operations toconnect them into chemically complete molecules and ions.The exception is where a molecule possesses crystallographicsymmetry, but the asymmetric fragment should still be a
 J. Appl. Cryst.
(2003).
36
, 7±13 A. L. Spek
Single-crystal structure validation
9
research papers

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