This example illustrates space group assignment in the presence of
pseudosymmetry and twinning.
The crystal structure of Ferrochelatase-1 (HemH) from Bacillus
anthracis (PDB code 2c8j) presented a moderately difficult
case for space group assignment. The lattice parameters, merging
statistics and systematic absences favoured the space group P21212.
A molecular replacement solution with a high contrast was found
using a search model generated from the PDB entry 1ak1 (sequence
identity of 73%). However, it was not possible to refine this
solution (the lowest value of R-free was about 40%). The structure
has been eventually solved, but in a monoclinic space group. In this
tutorial we follow the whole procedure including revision of space
2. Input data
The file hemh_unmerged.mtz contains unmerged HemH data
presented in the space group P222. As these are unmerged
data, the space group assignment only affects the order and indexing
of observations and can be altered with no loss of information using
pointless (the first program in aimless pipeline).
The file 1ak1.pdb was downloaded from the PDB and represents
a crystal structure of Ferrochelatase-1 from Bacillus subtilis
containing one protein molecule in the asymmetric unit. This
structure will be used as a search model for molecular replacement.
3. Structure solution
- Run aimless pipeline to identify bad images and
- Use the plot "R-merge vs. batch" for identifying bad
- Use the plot "R-meas vs. 1/resol^2" to identify resolution
- Rerun aimless pipeline with bad data removed
- Use controls in the folder "Exclude data" in aimless
- Check the space group assigned in the default aimless
- Try to solve the structure using molecular replacement, model
1ak1, and merged data from (2)
- Refine the structure (3) and take note of R and R-free,
examine the refined model vs. electron density maps. Is
there any potential for model improvement?
- Run aimless pipeline selecting the second hit
- Check "choose previous solution" check-box.
- In the folder "Choose solution": Select "Choose solution
from search by [Laue group solution number]" and type 2 in
the corresponding text box.
- check the space group assigned in this aimless run
- check if systematic absences along b are
- Solve the structure using molecular replacement, model 1ak1,
and merged data from (5)
- Refine structure from (6), examine model vs. map,
compare refinement statistics with one from step (4)