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 Icon
and 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 Shelx
output.
Typical SHELXL RUN
Floating origin restraints generated
7056
Reflections read, of which
-10 =< h =< 10,
0
-6 =< k =< 10,
995
rejected
-13 =< l =< 13, Max. 2-theta =
50.70
Systematic absence violations
Inconsistent equivalents etc.
h
k
l
Fo^2
6
5
0
0
1
5
51141.65
32120.26
2
2683
Sigma(Fo^2)
212.72
232.67
N
3
3
Esd of mean(Fo^2)
1812.89
1444.75
Inconsistent equivalents
Unique reflections, of which
R(int) = 0.0166
R(sigma) = 0.0250
Maximum memory for data reduction =
0
suppressed
Friedel opposites not merged
2400 /
26284
To get a low Rmerge you need to have the crystal standing
up 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 file
ACTA, SIZE, TEMP (ºC).
Use Oscail to Add/Replace the Space Group.
Start Oscail on the Diffo. And find the INS file for the JOB
Click 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.INX
Job.HKL
Job_od.CIF
Job.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 Open
The 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.
;