Electron density unexplained

The surprising feature of such a structure is the possibility of the occurrence of the /3-d anomer in the crystal. The electron density can be explained by the presence of 22% as the /3-d anomer it is indicated by the height of an unexplained peak near C-l at the correct distance and angle for the /3-D structure. When once-recrystallized 2-acetamido-2-deoxy-a-D-glucopyranose is dissolved, its initial rotation is [a]D +56.5°, as compared to +82° for the a-D and —21.5°... 

Finally, ordered water molecules were added to the model where unexplained electron-density was present in chemically feasible locations for water molecules. Temperature factors for these molecules (treated as oxygen atoms) were allowed to refine individually. If refinement moved these molecules into unrealistic positions or increased their temperature factors excessively, the molecules were deleted from the model. Occupancies were constrained to 1.0 throughout the refinement. This means that B values reflect both thermal motion and disorder (Section II.C). Because all B values fall into a reasonable range, the variation in B can be attributed to thermal motion. Table 8.2 shows the progress of the refinement. 

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