This example, EX_2 has the formula C₂₇H₂₀O₄Fe₂Sn and the structure shown here.


It is assumed that you have had a look at the EX_1 example

This example is intended for practice in solving and refining a structure.

Two files are provided ex_2.inx and ex_2.hkl. Start Oscail.

Use Select Job and Directory to point Oscail at the folder (\xlearn\ex_2) containing ex_2.inx file.
The status line should show Jobname ex_2 and the Current folder you are using.

DATA QUALITY and SPACE GROUP
Data quality and Space Group possibilities can be examined using the program ABSEN.
Determination of the correct Space Group is one of the most
important steps in determining a crystal structure.
Select Run Job and Absen and when Absen starts select Data_Quality on the menu.



This plot shows the fraction of observed data plotted against resolution. The data is very good.

Select Space Gr. from Absences on the menu and you should get

The Space Group is clearly P2₁/n (a non-standard setting of P2₁/c No. 14) and it will be selected when you click OK.

STRUCTURE SOLUTION
Select Run Job and SHELXS-97

Select Yes on Review Screen Output and OK.

You will see that the CFOM is a satisfactory 5.4%.  It is difficult to generalize but the
following may be useful
a CFOM of >0.18 is unlikely to be correct
a CFOM 0f <0.01 could indicate trouble.



It is also clear that the two Fe atoms and the Sn have been located.
Select No to Review Screen Output and select defaults until dialog10 appears.



Set the number of peaks to 3 as two Fe and one Sn will easily produce a reasonable map. Select defaults until the picture appears in ORTEX it should look like.



Click Shelxl on the menu to refine the three atoms and use defaults back to ORTEX click the Ed button to to into Edit mode and then click Add-2-INS / ANIS on the menu. Click the right mouse button to exit Edit mode (making the heavy atoms anisotropic will prevent intense shadows appearing close to the heavy atoms). Run Shelxl again and when you return to ORTEX select Review Peak List on dialog10.



Notice that peak Q32 is weaker than Q32. Set the number of peaks to 31 and click OK.



All the non-H atoms are now located. Click Shelxl to refine the structure. Notice that the bond lengths improve.
In Edit mode click Add-2-INS / ANIS on the menu, click the right mouse button to exit Edit mode and run Shelxl again. The R factor is now 4.65% and all that remains is to name the C and O atoms and add the hydrogens.

Do this in Edit mode. Select an atom with a left mouse click and press c/C (to change) in this case C1 was the first atom.



If you press n/N when an atom is selected then the last atom number is incremented. When you have finished click the right mouse button.



Click Yes on the dialog and run Shelxl.
To add the hydrogens to the ring carbons in Edit mode select Add-2-INS / HFIX on the menu and select the default 43 type. Select a ring carbon which should have a hydrogen with a left mouse click and press h/H and the atom name should go blue. When all of the 43 type have been selected click the right mouse button and run Shelxl. Use the same procedure to add the 23 type to C6.
Run Shelxl and then use Add-2-INS / WGHT Qs with defaults to "move up the WGHT". The final Shelxl run should be -



and the R is now 3.15%. You can add centroids in Edit mode and "bond them" to the Fe atoms by clicking in Type 1 dashed contacts to give the final atom mode picture.

The total time to go from STRUCTURE SOLUTION to this point should be (with practice) less than 5 mins 

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