Antiparallel model

Rpl =0.179, Rp2 = 0.202, Ral =0.207, and Ra2 = 0.249. Statistical tests show that model a2 can be rejected in favor of aj. The choice between the parallel models pj and p2 is more difficult but examination of model p2 shows that this model cannot be fully hydrogen bonded, and hence p2 is rejected in favor of pj, which also gives better x-ray agreement. Thus models pj and aj were taken as the most likely parallel and antiparallel models for further refinement. At this point the unobserved data were included, calculating weighted R and R" where w = l for observed and w=l/2 for unobserved reflections. F(hkl) for an unobserved reflection was set at two thirds an assigned threshold and was included only if the calculated structure amplitude exceeded the threshold. The final residuals for the two models were Rpi = 0.233, R = 0.299, and Rj = 0.215, R j = 0.270. Application of the Hamilton statistical test (13) to these data indicates that the a model can be rejected at the 99.5% level. 

The defects in the model could not be overcome with the P212 121 space group and it was necessary to consider the lower symmetry, P2i. Refinement was attempted for both parallel and antiparallel chain models. At this point it was found that the data was not sufficiently sensitive to allow simultaneous refinement of more than six variables, and it was necessary first to refine the 1, 2, S, K, and B, and then consider the other variables. The best parallel chain model obtained had R" = 0.25, which could easily be rejected in favor of an antiparallel model at R"=0.16. The 1, 2, and S parameters refined for the antiparallel P2j model were not significantly different from those for the P2 j2 j2 j model. 

A new coiled coil model system was designed so that the fluorinated peptide interacted with an exclusively native interaction partner that, itself, was not intrinsically affected by fluorine. Therefore, the folding specificity of the coiled coil system had to be reversed by design. The question was whether the findings for this new model system would be comparable to those for the antiparallel model system described in the preceding sections. 

Table VI shows that the data sets do produce slightly different structures. The SRRC program was used with the RMF and MGW data sets and the Sarko-Muggll (22) monomeric coordinates to determine the best values of chain rotation, translation and 06 rotation (06 was restricted to the tg range of positions) for up, down and antiparallel models. The scale factors ranged between 0.7 and 1.0.

We have refined several parallel-up and antiparallel models against the diffraction data and the best agreements between the calculated and the experimental data are shown in Figures 4 and 5. The and projections of the corresponding models are shown in Figures 6 and 7. 

Figure 5. Calculated and observed patterns for the best antiparallel model. The observed pattern Is shown by dots with vertical bars based on counting statistics. The calculated pattern Is shown by a continuous curve in the same field and the difference between the observed and the calculated patterns Is...

Figure 7. Best antiparallel model obtained from Rietveld refinement against observed pattern (R - 0.226). a) be projection b) ab projection. All the carbon and the oxygen atoms are shown for one corner and one central molecule only, in the unit cell. Only the oxygen atoms are shown for other molecules.

Table III. Fractional and cartesian coordinates of the best antiparallel model. Species 1 is oxygen and species 2 Is carbon. The first 45 atoms cire in the corner molecule and the rest are in the center molecule. In each tetramer the first three monomers consist of 6 carbon atoms and 5 oxygen atoms and the monomer at the reducing end has 6 carbons and 6 oxygens...

Figure 11. Calculated diffraction patterns for parallel and antiparallel models refined against each other. The pattern for the parallel models is given by dots. The pattern for the antiparallel model is given by the continuous curve in the same field. The difference is shown in the lower field.

X-ray powder diffraction data indicate that the unit cell for cellotetraose is triclinic (space group PI) with two tetramers per unit cell. Although there is a small preference for a parallel structure at this stage, similarities between patterns calculated for parallel and antiparallel models make it difficult to choose one over the other. In addition to the rather insensitive R values, the differences in specific reflections in the observed and the calculated patterns for different models may be used as criteria in selection of a model. 

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