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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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