Crystallographic Preliminaries

For the purposes of the discussion given here, we will only consider point defects in crystalline solids. Our main objective in this section is to provide the semantic backdrop for the remainder of the chapter. Our starting point is the perfect crystal since this is the reference state against which the defected crystal is measured. In fig. 7.9, we provide a visual catalog of some of the key types of point defects that can perturb the uninterrupted regularity of the perfect crystal. 

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Table 2 shows the results of our preliminary calculations of the pKa of the Cys403 residue, for several different models of the enzyme, based on two structures available from the PDB. In the case of the YPT structure, a crystal water molecule is close to Cys403 and was included in some of the calculations as part of the protein (i.e. it was treated with the same internal dielectric as that of the protein). Simulations denoted as -I-H2O in Table 2, include a crystallographically resolved, buried water molecule, situated 3.2lA from... 

K.M. Beem, J.S. Richardson, and D.C. Richardson, Manganese, superoxide dismutases from Escherichia coli and from yeast mitochondria preliminary x-ray crystallographic studies. J. Mol. Biol. 105, 327-332 (1976). 

Evaluation of the morphology of a pharmaceutical solid is of extreme importance, since this property exerts a significant influence over the bulk powder properties of the material. In addition to providing insights into the micromeritic properties of the solid, microscopy can also be used to develop preliminary estimations of the particle-size distribution. A determination can be easily made regarding the relative crystallinity of the material, and it is often possible to deduce crystallographic information as well. Unknown particulates can often be identified solely on the basis of their microscopic characteristics, although it is useful to obtain confirmatory support for these conclusions with the aid of microscopically assisted techniques. 

H. Kuhl, J. Kruip, A. Seidler, A. Krieger-Liszkay, M. Bunker, D. Bald, J.A. Scheidig, M. Rogner (2000) Towards structural determination of the water-splitting enzyme. Purification, crystallization, and preliminary crystallographic studies of photosystem II from a thermophilic cyanobacterium. J. Biol. Chem., 275 20652-20659... 

CopperdI) dimethyl sulfoxide complexes [Cu(Me2SO)n]2+ n = 4 (309, 391) n = 5 (496) n = 9 (221)] have been synthesized and assigned as O-bonded by spectroscopic study. The Ph2SO complex [Cu(Ph2SO)4]2+ (228) has been prepared and isolated as its perchlorate salt. Preliminary crystallographic data (320) and ESR data (483) are available which suggest D4h symmetry for the metal-ion site. 

Crystallization is the technique that most noncrystallography laboratories can easily carry out in the initial stages of a structural study. Crystallization experiments, for the most part, can be carried out without much expense or technical knowledge. Many proteins give preliminary crystals following the techniques outlined below, and anyone who approached a crystallographer with crystals in hand would quickly find a welcome reception. 

The biological relevance of this histone variant has already been discussed in Section 2.2. As it was pointed out there, the recent crystallographic structure [41] of a nucleosome containing recombinant H2A.Z (rH2A.Z) revealed structural features that pointed towards a nucleosome destabilizing role for this histone variant (see Fig. 9A-B). Two recent papers [42,375] have pursued the preliminary findings established by this paper and proceeded with the structural characterization of chromatin complexes in solution. 

Krengel, U., Dey, R., Sasso, S., Okvist, M., Ramakrishnan, C. and Kast, P. (2006). Preliminary X-ray crystallographic analysis of the secreted chorismate mutase from Mycobacterium tuberculosis a tricky crystallization problem solved. Acta Crystallogr. F 62, 441 45. 

Reinisch, K. M., Chen, L., Verdine, G. L. and Lipscomb, W. N. (1994). Crystallization and preliminary crystallographic analysis of a DNA (cytosine-5)-methyltransferase from Haemophilus aegyptius bound covalently to DNA. J. Mol. Biol. 238, 626-629. 

Tamulaitiene, G., Grazulis, S., Janulaitis, A., Janowski, R., Bujacz, G. and Jaskolski, M. (2004). Crystallization and preliminary crystallographic studies of a bifunctional restriction endonuclease Eco57I. Biochim. Biophy. Acta 1698,251-254. 

Lacking complete information on a given system, there are other avenues available for the preliminary investigation of the phase diagram. A thorough search of the literature may turn up individual phases in the system. While we have not yet reviewed X-ray crystallography, there are several crystallographic databases that provide valuable information. The first of these is the... 

Crystallographic data have not yet been reported for one of the four hexuloses, namely, D- or L-psicose, not yet crystallized. Preliminary results are available for /3-D-fructopyranose.18a As expected, the sugar has the 1C (d) conformation. The hemiacetal group on C-2 is not bound to a hydrogen atom, whereas 0-6 is linked to two hydrogen atoms. 

Schreuder H, Arkema A, deBoer B, Kalk K, Dijkema R, Mulders J, Theunissen H, Hoi W. Crystallization and preliminary crystallographic analysis of antistasin, a leech-derived inhibitor of blood coagulation factor Xa. JMol Biol 1993 231 1137-1138. 

Since the four yeast PGK inhibitors are commercially available it was logical to test them for T. brucei PGK inhibition. The first three compounds were active in the millimolar range. However, SPADNS exhibited a K of 10.0 pMin these in preliminary tests [88]. Moreover, when assayed against a commercially available rabbit muscle PGK, SPADNS had no influence on the enzyme kinetics up to a concentration of 250 pM[88], In conclusion, SPADNS appears to be an excellent lead because of its potency and selectivity. Crystallographic experiments to determine its binding mode to I brucei VGK are underway. 

Wright CE, Laver WG. Preliminary crystallographic data for influenza vims neuraminidase heads JMol Biol 1978 120 133-136. 

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