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:
Alexander J. Blake, University of Nottingham, UK
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
G. Pattenden (Nottingham)
etc, etc, etc
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
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
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
G General issues – check
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
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
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
- should do its own validation
A visual examination can often be revealing: here there are some extreme ellipsoids which are also incompatible with a rigid bond model
… in fact the bond lengths match the values expected
P.J. Cox, RGU, Aberdeen
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?
permits automated validation
We try to be helpful and informative !
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.
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.
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
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
Tony Linden (Zurich)
2002: 58% passed as is
97% of all submissions reach a Co-editor
but a mythology has grown up...
“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
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.
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 ...
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
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.
“Datasets must be (almost) perfectly
Reality: A dataset need only be essentially complete to 2 of ca. 50°/Mo, and thereafter have good completeness up to the diffraction limit.
? so what do authors do ?
1. Briefly in any experimental footnote
3. In any other Supplementary Data
; 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.
(automatic validation will not catch every problem)
Example: High ADPs on isolated atom
Atom is probably O rather than Cl
C-C range is 1.49 to 1.60 Å
However, C-C single bonds are found within this range
_chemical_formula_sum 'C24 H12 Fe O6'
Prior chemical information: Complex is either Ru/Ru or Ru/Zn
Refinement as Ru/Ru gave R1 = 0.064; unusual five-coordinate Ru geometry
could only be resolved using F maps
M. Schröder (Nottingham)
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)
Ln = Er, Tm or Yb ?
Z = 68, 69, 70
Similar geometry parameters
Crystallography is not much good at distinguishing these metals
_diffrn_radiation_source 'fine-focus sealed tube'
'SMART 1k on Daresbury SRS Station 9.8'
*see W. Clegg, Acta Cryst. 2003, E59, e2-e5
1. Overview of validation and checking
2. Validation for IUCr journals
3. Validation for chemical journals
4. The limits of validation
..... ..... .....