Incorrect crystal structures

These were largely due to inappropriate use of the method being applied. For the Rietveld based techniques, these errors included (i) entry of incorrect crystal structure information, including atom coordinates and thermal vibration parameters, (ii) incorrect space group notation, (iii) incorrect atom site occupation parameters, (iv) allowing structure parameters (especially thermal parameters) to refine to physically unrealistic values, and (v) not completing the refinement. 

Traditionally, least-squares methods have been used to refine protein crystal structures. In this method, a set of simultaneous equations is set up whose solutions correspond to a minimum of the R factor with respect to each of the atomic coordinates. Least-squares refinement requires an N x N matrix to be inverted, where N is the number of parameters. It is usually necessary to examine an evolving model visually every few cycles of the refinement to check that the structure looks reasonable. During visual examination it may be necessary to alter a model to give a better fit to the electron density and prevent the refinement falling into an incorrect local minimum. X-ray refinement is time consuming, requires substantial human involvement and is a skill which usually takes several years to acquire. 

If it were not for a number of crystal structures that unambiguously confirmed the structures of the products, it would be easy to believe that some of the structural assignments were incorrect. At present no completely satisfactory explanation for these results is available. Examples of the reactions with esters are given in Scheme 21. 

The biosynthetic pathway from a lycopodine derivative to serratinine 4 was proposed previously (a) Inubushi Y, Ishii H, Yasui B, Harayama T (1966) Tetrahedron Lett 7 1551 (b) Inubushi Y, Ishii H, Yasui B, Harayama T (1968) Chem Pharm Bull 16 101 (c) the references in (a) and (b) both have the incorrect stereocenter at C4. This was not established unambiguously until a crystal structure of a derivative was obtained see [4c]... 

Leading theoreticians were, however, attracted to the phenomenon and soon suggested models for F centers. In 1930 Frenkel suggested that an F center was an electron trapped in a distorted region of crystal structure, an idea that was incorrect in this instance but led directly to development of the concepts of excitons and... 

Crystal structures and crystal lattices are different, although these terms are frequently (and incorrectly) used as synonyms. A crystal structure is built of atoms. A crystal lattice is an infinite pattern of points, each of which must have the same surroundings in the same orientation. A lattice is a mathematical concept. 

Trypsin in which Asp 102 has been replaced by Asn has 1 ()4 times less catalytic activity than natural trypsin at neutral pH. From the crystal structure of the mutant enzyme it appears that the imidazole group of His 57 is held by the Asn side chain in the wrong tautomeric form for catalysis. Explain. Compare this incorrect tautomeric form with that in the initial structure shown in Fig. 12-11. 

D. A. House and B. R. Penfold, unpublished X-ray crystal structure. This implies that the a configurational assignments in ref. 740 are incorrect. 

Figure 8 Crystal structure of BANA113 bound to influenza virus neuraminidase. Docked conformations ranking first (correct) and eleventh (incorrect) in a DOCK/PMF score docking experiment are compared to the crystallographic binding mode.

On the basis of this argument and the known crystal structures of parents and oxidized products, Ni(dpg)2I and Pd(dpg)2I are metal oxidized while Ni(bqd)2I0.52 is ligand oxidized. Clearly, this argument ignores crystal packing considerations and may well be incorrect. 

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