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Validation and checking of crystal structures. Alexander J. Blake, University of Nottingham, UK and Anthony Linden, University of Zurich, Switzerland . This presentation contains material from the following lectures:

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validation and checking of crystal structures
Validation and checkingof crystal structures

Alexander J. Blake, University of Nottingham, UK

and

Anthony Linden, University of Zurich, Switzerland

This presentation contains material from the following lectures:

American Crystallographic Association Annual Meeting, Los Angeles, July 2001; International Union of Crystallography Congress, Geneva, August 2002; University of Natal, Pietermaritzburg, South Africa, August 2003; ACS 226th National Meeting, New York, September 2003; British Crystallographic Association, Chemical Crystallography Group Meeting, Cambridge, November 2003; European Crystallographic Meeting, Budapest, August 2004

slide2

How do we know whether this structure is correct and reliable?

G. Pattenden (Nottingham)

outline
OUTLINE
  • Overview validation and checking
  • Validation for Acta C, etc
    • Myths and misunderstandings
  • Validation for other journals
  • The limits of validation
slide4

Validation involves comparison against a set of test criteria

  • Do cell volume and cell parameters match?
  • Do bonded atoms have compatible Uij values?
  • Has the refinement converged?
  • Is the space group correct?
  • Are the assigned atom types correct?

etc, etc, etc

valid ation

Valid-ation

Correct

Appropriate

Defensible

checking is additional to validation
Checking is additional to validation
  • Does the structure make sense to you?
  • Does the structure look right?
  • Do chemically equivalent bonds agree?
  • Are all CIF entries complete and correct?
automated data validation with checkcif or platon
Automated data validation with checkCIF or PLATON
  • Checks for
    • CIF construction and syntax errors
    • missing information
    • parameters outside expected norms
    • conformation with convention
alert levels
ALERT LEVELS
  • A Serious – attention essential
    • Item omitted or large deviation from norm

Alert ANo crystal dimensions have been given

Alert ARatio of Tmax/Tmin expected is > 1.30 An absorption correction is required.

Alert A Atom C58A ADP max/min Ratio 18.00

slide9

ALERT LEVELS

  • B Significant – action needed?
    • Item is a significant or unexpected outlier

Alert BThe formula has elements in wrong orderAlert BADDSYM detects Cc to Fdd2 transformationAlert BRefined extinction parameter < 1.9sAlert BStructure contains VOIDS of 130.00 Å3

slide10

ALERT LEVELS

  • C Outside expected norms – examine
    • May appear trivial, but do not dismiss out of hand
    • - an extensive list may indicate problems

Alert CMoiety formula not givenAlert CShort inter X...Y contact: O7...C1 = 2.96 ÅAlert CLow U(eq) as compared to neighbors: C1Alert CD-H without acceptor N2–H2 ?

C1 and N2 should be N and C, respectively

slide11

ALERT LEVELS

G General issues – check

ALERT_3_G 

The ratio of expected to reported Tmax/Tmin (RR') is < 0.75

Tmin and Tmax reported:      0.062     0.155

Tmin' and Tmax expected:     0.385     0.609

RR'       0.633 

Please check that your absorption correction is appropriate.

380 ALERT4CLikely Unrefined X(sp2)-Methyl Moiety .... C18

412 ALERT2CShort Intra XH3 .. XHn:H19B .. H30A = 1.81 Ang.

720 ALERT4CNumber of Unusual/Non-Standard Label(s) .... 1

slide12

A/B/C indicate the seriousness of the problem

ALERT Type 1:

CIF construction/syntax error, inconsistent or missing data

ALERT Type 2:

Indicator that the structure model may be wrong/deficient

ALERT Type 3:

Indicator that the structure quality may be low

ALERT Type 4:

Cosmetic improvement, query or suggestion

Not all combinations are logical, for example 4 A

sources of outlier parameters
Sources of outlier parameters
  • Unresolved feature (e.g., untreated disorder)
  • Artefact due to limited data quality
  • Inadequate procedures (e.g., poor corrections)
  • Incorrect structure (e.g., wrong space group)
  • A genuinely unusual observation!!
what does validation software do

What does validation software do?

  • Identifies possible problems via ALERTs
  • Provides explanations of ALERTs
  • Suggests interpretations and possible solutions
  • Not just for authors
      • referees use it for assessment
      • authors need to be aware of this
      • how appropriate are IUCr criteria?
when to validate
When to validate?
  • software for data collection, refinement, etc

- should do its own validation

  • use PLATON in final stages of determination
  • validate raw CIF from the refinement program
  • must validate the final version as well
  • avoids problems at submission, refereeing, etc
looking at the structure
Looking at the structure

A visual examination can often be revealing: here there are some extreme ellipsoids which are also incompatible with a rigid bond model

slide18

1.369 Å

1.441 Å

1.390 Å

1.897 Å

… in fact the bond lengths match the values expected

Br

P.J. Cox, RGU, Aberdeen

slide19

Less satisfactory

Ordered t-butyl group has all C-C distances around 1.52 Å

Within the disordered group the range is 1.49 to 1.60 Å

Need (better) restraints?

Anon

validation checking procedure
VALIDATION/CHECKING PROCEDURE
  • Check the CIF from refinement using PLATON
  • Augment CIF using e.g. XCIF and enCIFer
  • Re-check the CIF using PLATON or checkCIF
  • Look at ellipsoid plots from several directions
  • Check bond lengths are sensible and consistent
  • After any changes, re-check the CIF
pre electronic times
Pre-electronic times
  • Results tables largely created by hand
    • only manual checking (if any)
    • laborious and time-consuming
    • hard to ensure consistent treatment
    • vital matters were easily overlooked
    • any revisions required laborious re-checking
early 1990 s cif introduced
Early 1990’s - CIF introduced
  • allows automatic creation of tables
  • enables full electronic submission/processing
  • increases efficiency, faster publication times
  • automates many editorial tasks
  • improves appearance of the journal

 permits automated validation 

automation of syntax and data checks
Automation of syntax and data checks
  • authors get instant, anonymous feedback
  • can detect and fix problems before submission
  • fewer, shorter revision cycles
  • consistent application of acceptance criteria
  • editors/referees can focus on science
  • RESULT: faster publication times
slide26

If you still get A alerts

  • is there a soundscientificbasis for the outlier?
  • put Validation Response Form (VRF) into CIF
  • submit CIF
  • CIF  Validation Co-editor (Acta C) Co-editor (Acta B or Acta E)
assessment of vrf
Assessment of VRF
  • VRF allows for “fine-tuning”
  • validation criteria need some flexibility
  • looking for sound scientific reasoning
  • sound explanation? Pass the CIF
  • otherwise suggest possible remedial action

We try to be helpful and informative !

slide28

A valid riposte

Alert B

ADDSYM detects additional (pseudo)

symmetry element: I

Author Response:This additional symmetry element does not hold true for one of the ether bridges, as discussed in the text.

slide29

An inadequate answer

  • Alert A < 85% complete (theta max?)
  • Author Response:Hemisphere of data
  • collected. [Space group P21/n, Nonius FAST]
  • But what is the reason for missing data:
      • inherent geometrical limitation?
      • mistake in data collection or reduction?
slide31

Just being helpful ...

Alert A Given & expected crystal density differ

Alert A Given & expected absorption coefficient differ

Calculated density = 3.377 density in CIF = 1.689

Calculated mu = 2.063 mu in CIF = 1.031

Author Response: It appears that the absmu- and the density-problem are related. No explanation other than it is related to the disordered triflate groups and the refinement over several partially occupied sites.

Cause of Alert: Molecule sits over an inversion centre in P21/n: Z given as 4, instead of 2.

how to get a cif through
How to get a CIF through
  • Give ALL Alerts due consideration
    • appreciate validation criteria
    • criteria are based on normally expected results from routine analyses
    • Why, then, is your structure not routine?
  • In any VRF...
    • avoid casual or circular responses
    • show you understand the causes of the outlier
    • explain why it is a true feature of the analysis
what causes most problems
What causes most problems?

VRN???01 Data completeness ALERT A probably spurious PASSED

VRN???02Space group ID is main subject of paper PASSED

VRN???03Some H atoms mistreated - authors to re-refineREJECT

VRN???0430 atoms isotropic in a very large structure PASSED

VRN???05 Coordinates/geometry mismatchREJECT

VRN???06 Max shift/su > 4.0 REJECT

VRN???07Perchlorate O atoms have extreme ADPs PASSED

VRN???08Atom labels randomly scrambled REJECT

VRN???09 Extreme H U values - inappropriate H atom treatment REJECT

VRN???10 Not a connected set? - probably a false positive PASSED

VRN???11 Central heavy atoms have high U wrt neighbors PASSED

common problems
Common problems ...

VRN???12 VRN???06 again; shifts now acceptable PASSED

VRN???13 H atom treatment; missing absorption correction REJECT

VRN???14 Solvent disorder modeling; high mean U3/U1 PASSED

VRN???15 VRN???09 again: still many problems with H atoms REJECT

VRN???16 VRN???09 again: nearly there PASSED

VRN???17 Spurious warning (intensity standards) but AD PASSED

VRN???18Ligands have geometric and Ueq problems PASSED

VRN???19 Problems with high U3/U1 PASSED

VRN???20 Dataset only 65% completeREJECT

VRN???21 Completeness: theta max was too high PASSED

VRN???22 Wide range of H-atom U values; very close H...H REJECT

common problems35
Common problems ...
  • Data completeness or resolution too low
  • Maltreatment of H atoms
  • Structure not at convergence
  • Missing or inadequate absorption correction
  • Indications of a poor structure
slide36

Acta C CIF submissions in 2000

Tony Linden (Zurich)

slide37

Fate of CIFs with VRFs in 2000

2002: 58% passed as is

validation is not a brick wall either to run into or get over
Validation is not a brick wall- either to run into or get over -

97% of all submissions reach a Co-editor

myths and myth understandings
Myths and myth-understandings
  • Introduction of validation:
  • Acta C electronic-only submission since 1996
  • are validation criteria widely understood?
  • explanations in Notes for Authors, etc

but a mythology has grown up...

slide41

Myth 1:

“Acta will not consider ‘problem’ or ‘difficult’ structures”

Reality: The problems or difficulties must be explained and justified

 disorder  twinning  crystal size  voids

 ADPs  pseudosymmetry  residual e-

 absorption  H atoms

slide42

Myth 2: “Acta will not publish any

structure with R1 > 0.05/0.07/0.10 ...”

Scylla

Reality: There is no formal cut-off, but a structure with a high R1 will need to be justified.

Abstract ...

2-(Di-n-propylamino)-8-hydroxytetralin (8OH-DPAT) hydrochloride,C16H26NO+Cl-, M = 283.8,monoclinic, P21/n, a = 9.9587 (7), b = 13.5746 (6), c= 12.1558 (6) Å,  = 94.537 (6)°, V= 1638.1 Å3, Z=4, Dx= 1.151gcm-3, (CuK)=l.54184Å,  = 19.00 cm-1, F(000) = 616, T= 298 K, final R =0.1781 with 1550 independent data. The structuresolution of 8OH-DPAT was hindered by the poorquality of the one crystal obtained ...

slide43

Myth 3: “Acta will not publish a structure with Z’ > 1 where one of the molecules is disordered”

Gorgon

Reality: We welcome such interesting structures, but the disorder must be treated adequately.

Acta Cryst. (1996). C52, 2814-2818

Two C-Unsubstituted Enaminals

Abstract

In both 3-(N,N-diisopropylamino)-2-propenal, C9H17NO, (3), and 3-(1,2,3,4-tetrahydro-l-quinolinyl)-2-propenal, C12H13NO, (4), the entire enaminal system(O1–C1–C2–C3–N4) is approximately planar. Theangles around the N atoms in (3) and (4) sum to valuesnear 360 °, indicating planarity in both molecules.Oneof the two crystallographically independent moleculesof (3) exhibits disorder in its isopropyl groups.

slide44

Myth 4:

“Datasets must be (almost) perfectly

complete”

Dragon

Reality: A dataset need only be essentially complete to 2 of ca. 50°/Mo, and thereafter have good completeness up to the diffraction limit.

_diffrn_reflns_theta_max 28.69

_diffrn_measured_fraction_theta_max 0.906

_diffrn_reflns_theta_full26.00

_diffrn_measured_fraction_theta_full 1.000

myth or not
Myth or not?
  • Is the assertion based on direct experience?
  • Check with Notes for Authors (www.iucr.org)
  • If in any doubt, ask a Co-editor (www.iucr.org)
  • Your case may not be the same as a similar one
checkcif in 2004
checkCIF in 2004
  • the new home of checkCIF: http://checkcif.iucr.org
  • service sponsored by ACS, CCDC and Elsevier
  • an ORTEP plot is now included
  • part of new Acta C/E submission procedures
  • will soon have online upload of all material for Acta C and E papers (CIF + figures/schemes/structure factors)
slide50

Standards, procedures vary widely

    • some journals perform extensive checks
    • some do only very basic checks
    • some do none at all

? so what do authors do ?

  • Perform your own validation
    • ensure there are no serious mistakes
    • ensure the quality is adequate
    • submit a copy of the checking report
example an acs procedure
Example – an ACS procedure
  • Authors submit the CIF along with the paper
  • CIF must contain author names and paper title
  • authorsmust have checked the CIF first
  • - the check report may be requested
  • reviewers have Web access to the CIF, along with the manuscript and any supplementary data
other procedures
Other procedures
      • Submit paper to journal
  • get a code for the paper
  • submit CIF under this code
      • Submit CIF to CCDC or ICSD
  • get deposition number
  • include number in paper
slide53

If you have a “difficult” structure

  • Identify and describe the problem
  • Give details of the remedial action taken
  • Describe the (successful?) outcome
slide54

Where and how?

1. Briefly in any experimental footnote

  • At the top of the CIF
  • use _refine_special_details

3. In any other Supplementary Data

example of text
Example of text

_refine_special_details

; Disorder was identified in one of the tetrafluoroborate anions.

All the F atoms were affected and two orientations were identified.

Similarity restraints were applied to B-F distances, and to F-B-F angles. All F atoms were refined isotropically. The occupancies of each group of four partially-occupied F atoms were refined competitively using a free variable. Each F atom was found to be disordered over two equally occupied sites, as shown by the final group occupancies of 0.506(12) and 0.494(12).

In the final model the range of B-F distances was 1.31(2)-1.42(2) Angstroms and the F-B-F angles spanned 105(2)-112(2) degrees. No difference Fourier peak in the region exceeds 0.6 e/A**3.

;

the limits of validation
The limits of validation

(automatic validation will not catch every problem)

possible limits to validation
Possible limits to validation
  • test not (yet) implemented
  • test not practical
  • error not a validation issue
  • error cannot be detected from data in CIF
  • nonsense entries in the CIF
slide58

Test not implemented

Example: High ADPs on isolated atom

  • Not detected by
  • rigid bond test
  • atom type test
  • ADP ratio test

Atom is probably O rather than Cl

slide59

Test not practical

C-C range is 1.49 to 1.60 Å

However, C-C single bonds are found within this range

slide60

Error not a validation issue

_chemical_formula_sum 'C24 H12 Fe O6'

_exptl_crystal_description needle

_exptl_crystal_colour colourless

_exptl_crystal_size_max 0.28

_exptl_crystal_size_mid 0.24

_exptl_crystal_size_min 0.03

error not detectable from cif data
Error not detectable from CIF data

Prior chemical information: Complex is either Ru/Ru or Ru/Zn

Refinement as Ru/Ru gave R1 = 0.064; unusual five-coordinate Ru geometry

other examples
Other examples

AgCNAg link,

AgNCAg link

or disordered?

could only be resolved using F maps

M. Schröder (Nottingham)

model complexes for nife hydrogenase
Model complexes for [NiFe] hydrogenase

need good data to distinguish Ni and Fe by refinement

Ni (Z = 28) vs Fe (Z = 26)

Z/Z = 2/28

R1 < 4 Z ?

Use F maps to confirm

and when data are poor

M. Schröder (Nottingham)

lanthanide complexes
Lanthanide complexes

Ln = Er, Tm or Yb ?

Z = 68, 69, 70

Similar co-ordination

Similar geometry parameters

Crystallography is not much good at distinguishing these metals

slide67

Nonsense entries in the CIF*

_diffrn_ambient_temperature 293(2)

_diffrn_radiation_wavelength 0.69010

_diffrn_radiation_type synchrotron

_diffrn_radiation_source 'fine-focus sealed tube'

_diffrn_radiation_monochromator 'graphite'

_diffrn_measurement_device_type

'SMART 1k on Daresbury SRS Station 9.8'

*see W. Clegg, Acta Cryst. 2003, E59, e2-e5

unsuitable shelx t l 97 defaults
Unsuitable SHELX(T)L-97 defaults ?
  • space group notation
  • diffractometer
  • T = 293 K ?
  • absorption correction
  • total data collected
  • index limits
  • Rint
  • H atom treatment
  • weighting scheme
  • precision
  • structure solution
summary
SUMMARY

1. Overview of validation and checking

2. Validation for IUCr journals

3. Validation for chemical journals

4. The limits of validation

thanks to
Thanks to

..... .....

George Ferguson

Ton Spek

Peter Strickland

..... ..... .....