NUI, Galway X-Ray Diffraction Best Practice P. McArdle Feb 2010

1. Saving the X-ray Tube

2. Getting the most from your data

3. Large Unit Cell Parameter Problem (>45Å)

4. Using CheckCIF

1. Saving the X-Ray Tube

Use 50kV/40mA and automatic turn down to 20kV/5mA at the end of data collection

Right click X-Ray Button and select Generator Options

Select Use Generator Ramping at end of experiment and Turn Down.Click OK

2. Getting the most out of your data.Start a second instance of CrysAlis (An instance with no Diffo. Control Buttons)Click START STOP. Click Load New Experiment.Open your Data Set PAR file.

Click the top button on the left (Lattice Wizard)

Click the button beside the Peak Hunting Iconand select Peak hunting with user settings.This will overwrite any peak list

Select Traditional Peak Hunting and Use Background Correction and click OK

Select Unit Cell finding with options

Do not select Twin unless you want to do a Twin run

Click OK

Click Start Stop and select Data reduction with options

Click Next twice.

Select Follow model changes, Moderate wobbling

Click Finish

Check the Rmerge in Shelxoutput.

Typical SHELXL RUNFloating origin restraints generated

7056 Reflections read, of which 995 rejected

-10 =< h =< 10, -6 =< k =< 10, -13 =< l =< 13, Max. 2-theta = 50.70

0 Systematic absence violations

Inconsistent equivalents etc.

h k l Fo^2 Sigma(Fo^2) N Esd of mean(Fo^2)

6 0 1 51141.65 212.72 3 1812.89 5 0 5 32120.26 232.67 3 1444.75

2 Inconsistent equivalents

2683 Unique reflections, of which 0 suppressed

R(int) = 0.0166 R(sigma) = 0.0250 Friedel opposites not merged

Maximum memory for data reduction = 2400 / 26284

To get a low Rmerge you need to have the crystal standingup on top of the glass fibre.

3. Large Unit Cell Parameter Problem (>45Å)

This looks OK spots seem resolved but Detector Dist = 45mm and the c = 45Å and 49% indexation.

Further on in the data set the spots are not resolved.It is necessary to increase the resolution in 3 Dimensions x, y and z.If x and y are the coordinates on the detector then z is normal to the detector.

Solution: - Use a longer Detector Distance to increase xy resolution and a smaller oscillation angle to increase z resolution.At the start of the pre-experiment set Detector dist. to 70mm and click dc edit runs

Select all of the runs and click Global Width set it to 0.5º

This is the result using 70mm and 0.5 deg oscillation.

Indexation is now 90%

4. Using CheckCIF

Oscail can combine the CIF from ShelxL with the CIF from the Diffo.

When you have refined a structure using ShelxL you should have the following Commands in the INS fileACTA, SIZE, TEMP (ºC).Use Oscail to Add/Replace the Space Group.

Start Oscail on the Diffo. And find the INS file for the JOBClick the O_D item on the Oscail Menu

Oscail gives the following Message.

Click the Windows Explorer Button and you can copy the files to your memory stick. The files you need are:Job.INXJob.HKLJob_od.CIFJob.p4p (if you have indexed the faces)

Back on your own PC run CIFTAB in Oscail

Click OK

Add the Colour etc and make sure the hydrogen treatment is correct.Click OK

Find the CIF file written by the Diffo. And click OpenThe number of ?s left in the CIF is written to the screen this is usually 6.

You can use the Oscail file checker the ? Button to examine the CIF file.If you follow the defaults a typical output is: ################################################## The SHEL command has been used and the resolution has been limited to 0.8300 Angstroms sin(THETA/LAMBDA) = 0.6024 Acta.Cryst. require at least 0.6 THETA LIMIT = 25.3503 There are AFIX instructions in the INS file ################################################## A CIF file exists _diffrn_measured_fraction_theta_max 0.994 _diffrn_reflns_theta_full 25.35 _diffrn_measured_fraction_theta_full 0.994 >95% expected CIF contains _diffrn_reflns_theta_max 29.0786 This is greater than the SHEL limit################################################## Comments and/or advice SHEL 999 0.83 leaves SIN(theta)/lamda > 0.6 Your Flack is_refine_ls_abs_structure_Flack 0.02(4) If this is OK add the following after Flack in cif_chemical_absolute_configuration; absolute configuration established by anomalous dispersion effects in diffraction measurements on the crystal.;