Solving Centrosymmetric
Crystal Structures in
Non-Centrosymmetric
Space Groups
Michael Shatruk
September 12, 2011
Steps in X-ray single crystal experiment
1. Crystal selection (including unit cell determination).
2. Data collection.
3. Data processing:
• Integration (to assign intensity to each observed hkl spot)
• Absorption correction (to match intensities of equivalent reflections)
• Space group determination (XPREP)
• Structure solution (SHELXS)
• Structure refinement (SHELXL)
• Structure validation (Platon, IUCR checkcif)
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Step 3 – Data Processing
After integration and absorption correction, the space group is
determined with XPREP, which also writes SHELXS input files.
# reflections total
# reflections (strong)
Step a.
Determine the
lattice type
The options in square brackets are default ones.
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Step b.
Search for higher
metric symmetry
The table of possible
higher symmetries
Desired R(sym) < 0.10
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Step c.
Determine the
space group
Space group
determination options
In most cases, we use option [S].
Sometimes, we will choose to input the space group.
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Step c.
Determine the
space group
XPREP determines
the space group
Lattice type
Centrosymmetric?
Systematically absent
reflections allow locating
specific symmetry elements
All the information
gathered above is
used to derive the
possible space groups
Desired CFOM < 5 (the lower, the better)
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In most cases, the
option D can be skipped,
and we can proceed
directly to option C
Step d.
Molecular formula
This is painful!
Do this ahead of time
in your experimental
description in APEX,
and you won’t have to
enter the formula here!
Again, we skip D and
proceed directly to F
Option F sets up the input file for structure solution in SHELXS.
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Step e.
SHELXS input
Choose an appropriate
filename (e.g., I prefer to
use the corresponding
space group symbol)
This is the
SHELXS input file
Usually we overwrite the
hkl file (intensity data)
Now we can quit,
although it is possible to
go back, if necessary
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Step c.
Determine the
space group
Now we choose to
input the space group
The symbol is not
case-sensitive
The systematic absences
statistics calculated for the
input space group
After this, choose option F
again to set up the SHELXS
input file with the newly
defined symmetry
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Important Points Regarding XPREP
1. In most cases, use defaults commands, but always beware
of what they are. Don’t just hit “Enter” without thinking.
2. Sometimes XPREP might now show you the correct space
group, and you might need to change the space group later
on, as you move on with the structure refinement.
3. It is better to set up all the possible space groups right
away, to save time and don’t need to use XPREP again.
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