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Solving Centrosymmetric Crystal Structures in Non-Centrosymmetric Space Groups. Michael Shatruk September 12, 2011. Steps in X-ray single crystal experiment. Crystal selection (including unit cell determination). Data collection. Data processing:

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solving centrosymmetric crystal structures in non centrosymmetric space groups

Solving Centrosymmetric Crystal Structures in Non-Centrosymmetric Space Groups

Michael Shatruk

September 12, 2011

steps in x ray single crystal experiment
Steps in X-ray single crystal experiment
  • Crystal selection (including unit cell determination).
  • Data collection.
  • 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)
step 3 data processing
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.
slide4

Step b.

  • Search for higher metric symmetry
  • The table of possible higher symmetries
  • Desired R(sym) < 0.10
slide5

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.
slide6

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)
slide7

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 skipD and proceed directly to F
  • Option F sets up the input file for structure solution in SHELXS.
slide8

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
slide9

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
important points regarding xprep
Important Points Regarding XPREP
  • In most cases, use defaults commands, but always beware of what they are. Don’t just hit “Enter” without thinking.
  • 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.
  • It is better to set up all the possible space groups right away, to save time and don’t need to use XPREP again.