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Validation and checking of crystal structures
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Validation and checkingof crystal structures
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
Alexander J. Blake, University of Nottingham, UKand
Anthony Linden, University of Zurich, Switzerland
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G. Pattenden (Nottingham)
How do we know whether this structure is correct and reliable?
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• Overview validation and checking• Validation for Acta C, etc
Myths and misunderstandings• Validation for other journals• The limits of validation
OUTLINE
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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
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Valid-ation
Correct
Appropriate
Defensible
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• Does the structure make sense to you?
• Does the structure look right?
• Do chemically equivalent bonds agree?
• Are all CIF entries complete and correct?
Checking is additional to validation
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Automated data validation with checkCIF or PLATON
• Checks for– CIF construction and syntax errors– missing information– parameters outside expected norms– conformation with convention
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A Serious – attention essentialItem omitted or large deviation from
norm
Alert A No crystal dimensions have been given
Alert A Ratio of Tmax/Tmin expected is > 1.30An absorption correction is required.
Alert A Atom C58A ADP max/min Ratio 18.00
ALERT LEVELS
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B Significant – action needed?Item is a significant or unexpected
outlierAlert B The formula has elements in wrong orderAlert B ADDSYM detects Cc to Fdd2 transformationAlert B Refined extinction parameter < 1.9sAlert B Structure contains VOIDS of 130.00 Å3
ALERT LEVELS
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ALERT LEVELS
C Outside expected norms – examineMay appear trivial, but do not dismiss out of hand
- an extensive list may indicate problems
Alert C Moiety formula not givenAlert C Short inter X...Y contact: O7...C1 = 2.96 ÅAlert C Low U(eq) as compared to neighbors: C1Alert C D-H without acceptor N2–H2 ?
C1 and N2 should be N and C, respectively
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ALERT LEVELS
G General issues – checkALERT_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 ALERT 4 C Likely Unrefined X(sp2)-Methyl Moiety .... C18412 ALERT 2 C Short Intra XH3 .. XHn:H19B .. H30A = 1.81 Ang.720 ALERT 4 C Number of Unusual/Non-Standard Label(s) .... 1
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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
A/B/C indicate the seriousness of the problem
Not all combinations are logical, for example 4 A
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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!!
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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?
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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
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A visual examination can often be revealing: here there are some extreme ellipsoids which are also incompatible with a rigid bond model
Looking at the structure
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A pretty picture, but what about the numbers …
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1.897 Å
Br
1.390 Å
1.441 Å1.369 Å
P.J. Cox, RGU, Aberdeen
… in fact the bond lengths match the values expected
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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
Less satisfactory
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1. Check the CIF from refinement using PLATON2. Augment CIF using e.g. XCIF and enCIFer3. Re-check the CIF using PLATON or checkCIF4. Look at ellipsoid plots from several directions5. Check bond lengths are sensible and
consistent6. After any changes, re-check the CIF
VALIDATION/CHECKING PROCEDURE
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Validation and IUCr Journals
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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
Pre-electronic times
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• 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
Early 1990’s - CIF introduced
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• 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
Automation of syntax and data checks
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Authors working
with CHECKCIF
Resolve alerts
A lerts p resent
Submissionprocessed normally
Submit to Cheste r
A lerts no t presen t
Submit to CHECKCIF
Prepare C IF
Crystal growthData co llection
RefinementStructure analysis
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• is there a soundsound scientificscientific basisbasis 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)
If you still get A alerts
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• 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 !
Assessment of VRF
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A valid riposte
Alert BADDSYM detects additional (pseudo) symmetry element: I
Author Response:This additional symmetry element doesnot hold true for one of the ether
bridges,as discussed in the text.
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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?
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How does it work?
Re-evaluateprojec t
Outliersnot justifiable
D isagrees Approves
Validation Editor
Include VRF& subm it
Sound reasonsfor ou tliers
A alertsstill presen t
P rocessednormally
Submit C IFto Cheste r
NoA A lerts
Best effortat resolving
A, B & C alerts
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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.
Just being helpful ...
Alert A Given & expected crystal density differAlert A Given & expected absorption coefficient differCalculated density = 3.377 density in CIF = 1.689Calculated mu = 2.063 mu in CIF = 1.031
Cause of Alert: Molecule sits over an inversion centre in P21/n: Z given as 4, instead of 2.
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• 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?
How to get a CIF through
• 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
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What causes most problems?
VRN???01 Data completeness ALERT A probably spurious PASSED
VRN???02 Space group ID is main subject of paper PASSED
VRN???03 Some H atoms mistreated - authors to re-refine REJECT
VRN???04 30 atoms isotropic in a very large structure PASSED
VRN???05 Coordinates/geometry mismatch REJECT
VRN???06 Max shift/su > 4.0 REJECT
VRN???07 Perchlorate O atoms have extreme ADPs PASSED
VRN???08 Atom 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
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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???18 Ligands have geometric and Ueq problems PASSED
VRN???19 Problems with high U3/U1 PASSED
VRN???20 Dataset only 65% complete REJECT
VRN???21 Completeness: theta max was too high PASSED
VRN???22 Wide range of H-atom U values; very close H...H REJECT
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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
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Acta C CIF submissions in 2000
20% with VRF
80% validTony Linden (Zurich)
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Fate of CIFs with VRFs in 2000
48% passed
as is
20% returnedas valid
16% passed on
next try
16% not resubmitted
2002: 58% passed as is
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All Acta C submissions in 2000
3% not resubmitted
10% with valid VRF
80% valid
7% valid after
revision
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97% of all submissions reach a Co-editor
Validation is not a brick wall
- either to run into or get over -
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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...
Myths and myth-understandings
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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
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Scylla
Myth 2: “Acta will not publish any
structure with R1 > 0.05/0.07/0.10 ...”
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= 1.151g cm-3, (CuK) = l.54184 Å, = 19.00 cm-1, F(000) = 616, T = 298 K, final R = 0.1781 with 1550 independent data. The structure solution of 8OH-DPAT was hindered by the poor quality of the one crystal obtained ...
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Gorgon
Myth 3: “Acta will not publish a structure with Z’ > 1 where one of the molecules is disordered”
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. The angles around the N atoms in (3) and (4) sum to values near 360 °, indicating planarity in both molecules. One of the two crystallographically independent molecules of (3) exhibits disorder in its isopropyl groups.
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Myth 4: “Datasets must be (almost) perfectly complete”
Reality: A dataset need only be essentially complete to 2 of ca. 50°/Mo, and thereafter have good completeness up to the diffraction limit.
Dragon
_diffrn_reflns_theta_max 28.69
_diffrn_measured_fraction_theta_max 0.906
_diffrn_reflns_theta_full 26.00
_diffrn_measured_fraction_theta_full 1.000
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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
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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)
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Validation and other Journals
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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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Example – an ACS procedure
• Authors submit the CIF along with the paper
• CIF must contain author names and paper title
• authors must 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
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Other procedures
• Submit paper to journalget a code for the papersubmit CIF under this code
• Submit CIF to CCDC or ICSDget deposition numberinclude number in paper
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If you have a “difficult” structure
• Identify and describe the problem
• Give details of the remedial action taken
• Describe the (successful?) outcome
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1. Briefly in any experimental footnote
Where and how?
2. At the top of the CIFuse _refine_special_details
3. In any other Supplementary Data
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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.;
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(automatic validation will not catch every problem)
The limits of validation
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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
Possible limits to validation
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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
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Test not practical
C-C range is 1.49 to 1.60 Å
However, C-C single bonds are found within this range
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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
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Prior chemical information: Complex is either Ru/Ru or Ru/Zn
Refinement as Ru/Ru gave R1 = 0.064; unusual five-coordinate Ru geometry
Error not detectable from CIF data
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Difference map with Ru/Ru model (R1 = 0.064)
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Difference map with Zn/Zn model (R1 = 0.022)
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AgCNAg link, AgNCAg linkor disordered?
could only be resolved
using F mapsM. Schröder (Nottingham)
Other examples
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need good data to distinguish Ni and Fe by
refinementNi (Z = 28) vs Fe (Z = 26)
Z/Z = 2/28
M. Schröder (Nottingham)
R1 < 4 Z ?
Model complexes for [NiFe] hydrogenase
Use F maps to confirm and when data are poor
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Lanthanide complexes
Ln = Er, Tm or Yb ?
Z = 68, 69, 70
Similar geometry parameters
Similar co-ordination
Crystallography is not much good at distinguishing these metals
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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
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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
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SUMMARY
1. Overview of validation and checking
2. Validation for IUCr journals
3. Validation for chemical journals
4. The limits of validation
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Thanks to
..... ..... George Ferguson
Ton SpekPeter Strickland
..... ..... .....