Combined Twinning and Disorder

1/5) Solve structure using SHELXT and ShelXle

To solve this structure we'll use SHELXT, while for model building and other visualization tasks, we'll use ShelXle. Instructions to solve the structure are in file sp02.ins, shown below:

Unlike most structure solution programs, SHELXT does not need to know the space group a priori. It works by first finding an expansion of the structure using space group P1 and then tries to assign the proper space group using the phases obtained for the P1 solution. In order to figure out the space group, however, it does need to know the Laue group. In the above file, LATT and SYMM indicate a primitive centrosymmetric monoclinic unit cell. Once the structure is solved, SHELXT will insert the required symmetry for P2₁/c as SYMM instructions.

SHELXT can be run from a command line or from the APEX3 GUI. For uric acid dihydrate, SHELXT gives three separate 'solutions', distinguished by the suffixes '_a', '_b', '_c' for space groups P2₁/c, P2₁, and Pc. Results for the P2₁/c structure are in file sp02_a.res, which looks like this:

Notice that the SYMM line now includes translations of a half for y and z, which are required for P2₁/c. Some diagnostics from the SHELXT run are also included on REM lines. At this stage, all of the atoms of the uric acid molecule and the two waters should be present. Although SHELXT tries to assign atom types based on elements present on the SFAC line and the amount of electron density it found, it does not always get all atoms correct, so a few of them might be mis-assigned. As with any other structure, we should fix any errors before moving on. If we load the structure into ShelXle, we should see something like this:

In the above ShelXle window, the two water molecule oxygen atoms were assigned by SHELXT to be nitrogen, and the atom labelled C008 ought to be nitrogen, not carbon. These are easily fixed in ShelXle. For example, the right mouse button brings up several options, one of which is "Change element to...". For this exercise, however, we'll jump straight into "Rename Mode" so that we can fix atom types and assign a sensible numbering scheme all at one go. We might as well also use ShelXle's SORT routine (it's in the SHELX dropdown menu). The result ought to look something like this:

It is always best practice to assign a sensible numbering scheme and to sort the list of atoms into a logical order. The ShelXle text editor on the right side of the above image shows the current SHELXL *.ins/*.res file.

In the next section we will account for twinning. In preparation for that, we'll run a few cycles of least-squares refinement with SHELXL, which gives us an idea of how lousy the fit is prior to modelling twinning and disorder. The result should look something like the following:

The ShelXle display also shows some difference map peaks. The largest of these are likely candidates for disordered atoms, but we'll ignore them for now. In section 2, we'll deal with the twinning problem.