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Validation and checking of crystal structures

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

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  1. 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

  2. How do we know whether this structure is correct and reliable? G. Pattenden (Nottingham)

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

  4. 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

  5. Valid-ation Correct Appropriate Defensible

  6. 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?

  7. Automated data validation with checkCIF or PLATON • Checks for • CIF construction and syntax errors • missing information • parameters outside expected norms • conformation with convention

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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!!

  14. 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?

  15. 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

  16. 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

  17. A pretty picture, but what about the numbers …

  18. 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

  19. 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

  20. 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

  21. Validation and IUCr Journals

  22. 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

  23. 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 

  24. 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

  25. Authors working with CHECKCIF

  26. 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)

  27. 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 !

  28. 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.

  29. 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?

  30. How does it work?

  31. 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.

  32. 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

  33. 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

  34. 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

  35. 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

  36. Acta C CIF submissions in 2000 Tony Linden (Zurich)

  37. Fate of CIFs with VRFs in 2000 2002: 58% passed as is

  38. All Acta C submissions in 2000

  39. Validation is not a brick wall- either to run into or get over - 97% of all submissions reach a Co-editor

  40. 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...

  41. 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

  42. 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 ...

  43. 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.

  44. 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

  45. 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

  46. 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)

  47. Validation and other Journals

  48. 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

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