Crystallography with a dual source diffractometer at Reading

1
Crystallography with a dual source diffractometer
at Reading Yu Gana, R. Jeremy H. Daviesb, Anna.
L. Brogdena, Abeer Naseera, Sayima. J. Ahmeda,
Christine. J. Cardina. aDepartment of Chemistry,
University of Reading, RG6 6AD UK. bSchool of
Biological Sciences, Queens University, Belfast
BT7 1NN UK E-mail scr03yg_at_reading.ac.uk
A newly installed diffractometer with facile
switching between copper and molybdenum sources
(0.7107Å) has made crystallographic studies at
Reading more versatile. The Rints of the data
collected with the molybdenum source very often
stay at around two percent, which makes structure
solution for difficult structures become
possible. For example, a data set with a Rint of
0.018 was collected on a crystal of complex
between theophylline and dimethyl sulfoxide (S1),
in which each theophylline molecule is hydrogen
bonded to one dimethyl sulfoxide (DMSO) molecule
through an N-HO hydrogen bond 1 . On other
two occasions where Br- (S2) or I- (S3) ions were
included in the structure as counter ions, the
absolute configuration of each chiral molecule
was determined with very reliable statistics, in
both cases, the Flack parameters were around
0.015.
The stronger copper source also makes it possible
to study structures of supramolecular crystals,
which very often have tiny crystal sizes. These
crystals, as well as being tiny, often have cell
dimensions extending
to 40-50Å or more, and the long wavelength of
copper can make the diffraction spots better
resolved. In one study, the 2-hydroxyphenyl
derivative of oxadiazolydiazenidol (1-) complex
was found to have great potential for
polynucleation chemistry, as the X-ray crystal
structure (S7) showed this complex could act as
an anionic, N-O chelating ligand analogous to
8-hydroxyquinoline 3. Two other organometallic
supramolecule structures are also presented (S8,
S9).
S1 S2 S3
Cell dimensions a10.108 b6.669Å c17.372Å ß94.000º a8.027Å b11.145Å c15.837Å a6.704Å b11.613Å c12.247Å
Spacegroup P21/c P212121 P212121
?(º) 3.0-30.1 2.2-28.9 2.4-33.5
Rint 0.018 0.052 0.040
Data/parameter 16.1 20.2 31.9
R Igt2s(I) 0.039 0.029 0.049
Flack n/a -0.0168 (0.0346) 0.0137 (0.0203)
  S7 S8 S9
? (Å) 1.5418 0.7107 1.5418
Cell dimensions a16.690Å b17.330Å c20.190Å ß90.540º a16.563Å b47.727Å c17.266Å ß90.492º a17.689Å b18.650Å c21.965Å a104.401, ß90.000, ?90.000
Spacegroup P21/c P21/c P-1
?(º) 5.5-54.2 2.1-26.0 3.5-62.8
Rint 0.206 0.069 0.064
Data/parameter 10.6 18.7 13.0
R Igt2s(I) 0.084 0.117 0.067
On the other hand, with a focused copper source
(1.5418Å) also available, the determination of
the absolute configuration of typical organic
molecules can be routinely carried out. An
excellent example is the high resolution crystal
structure of the intramolecular thymine-adenine
photoadduct d(TpA) (S4), in which the absolute
configuration at the original thymine C5 and C6
atoms confirms the hypothesised photoaddition
mode that should be favored by the stacked
thymine and adenine bases in B-DNA. All hydrogen
atoms were readily located. 2 Two other pure
organic structures that have their absolute
configuration determined are also presented (S5,
S6).
Studies on DNA structures and their interactions
with small ligands, and protein crystal
engineering using lysozyme and thaumatin as the
subjects are also carried out. Nice results like
DNA-intercalator complexes, DNA Holliday
junctions formed by new sequences, and new A-DNA
structures are obtained on a regular basis. For
instance, a medium sized DNA crystal
(0.20.20.1mm) diffracted to 1.78Å, which
allowed a nice data collection with a Rint of
0.062. This DNA structure (S10) with a large cell
of a65.971Å, b24.179Å, c73.890Å, ß110.370
was later solved by a rigid body search of
REFMAC5 and revealed a Holliday junction formed
by a new DNA sequence. The data statistics are
listed in the following table.
S4 S4 S5 S6
Cell dimensions a8.327Å b10.732Å c33.128Å a8.327Å b10.732Å c33.128Å a7.313Å b9.813Å c37.835Å a12.983Å b6.819Å c15.158Å ß114.220º
Spacegroup P212121 P212121 P212121 P21
?(º) 3.0-62.4 3.0-62.4 4.7-58.9 3.2-62.8
Rint Rint 0.032 0.025 0.021
Data/parameter Data/parameter 16.1 9.7 10.5
R Igt2s(I) R Igt2s(I) 0.028 0.047 0.032
Flack 0.000 0.000 0.0148 (0.0378) 0.0181 (0.1334)
Resolution (Å) Average redundancy Completeness () Mean F2/sF2 Rint Rsigma
4.16-3.29 5.5 99.67 12.27 0.039 0.044
2.26-2.14 3.2 97.91 2.64 0.176 0.198
1.96-1.78 1.3 94.74 1.76 0.211 0.216
Inf-1.78 3.9 98.04 11.44 0.062 0.081

• References
• Cardin, J. C., Gan. Y., Lewis, T. (2007) Acta.
  Cryst., E63, o3175.
• Davies, R. J. H., Malone, J. F., Gan, Y., Cardin,
  C. J., Lee, M. P. H., Neidle, S. (2006), Nucleic
  Acid Res, 35, 1048-1053.
• Colquhoun, H. M., Chan, S. Y. F., Cardin, C. J.,
  Drew, M. G. B., Gan, Y., Kader, K. A. E. and
  White, T. M. (2007) Dalton Trans., Accepted.

Acknowledgments We thank BBSRC and EPSRC for the
financial support of this work.
All data reported here were collected on the
Oxford Diffraction Gemini-S-Ultra diffractometer
in the Department of Chemistry, University of
Reading.