Experiment 4: Identification of bound solvent ions
In this experiment, the solvent structure around tetragonal hen egg white lysozyme will be examined. Recently, it has been reported based on diffraction data collected at longer X-ray wavelengths, that most macromolecular crystal structures contain some sort of solvent ions more or less tightly bound to their surface. This is in stark contrast to the findings in the Protein Data Bank (PDB), where in most cases only water molecules were modelled to be bound to the surface of the crystallized macromolecules and it suggests that in many structures surface bound ions might have mistakenly been assigned as water molecules.
By examining the anomalous difference electron density map based on data collected at longer wavelength (in this particular case at λ = 1.5418 Å), at which the anomalous signal of the light atoms, such as S, Cl etc. is enhanced, up to 10 Chloride ions can be identified as bound to the protein surface. Needless to say, all the protein S-atoms appear as peaks in the anomalous difference electron density map as well.
- Download the Tutorial as a pdf file (380 KB)
- Download the diffraction images 1/3 (615 MB)
- Download the diffraction images 2/3 (620 MB)
- Download the diffraction images 3/3 (620 MB)
- Download the data processing (43.5 MB)
- Download the structure solution (5.0 MB)
- Download the refined structure (pdb) and structure factors (mtz) (550 KB)