“the training of a crystallographer frequently reminds me...
TRANSCRIPT
“The training of a crystallographer frequently reminds me of that of a Jedi Knight: the practical knowledge only goes from the master’s mouth to the apprentice’s ear (…)Even though the lack of Jedi Knights may be more obvious in our society than the lack of good crystallographers, I think this book will be a helpful tool for many structurally active scientists.“
(Peter Müller, 1998)
Introduction
ANODE calculates anomalous or heavy atom density.
φA = φ T – α φA
|FA| anomalous/heavy atom density map
From SHELXC or XPREP
From PDB model
Marker atom:|FA| and φA
Macromolecule:|FT| and φT
Phase relation:φT = φ A + α
ANODE: general principle
ANODE proved to be a useful tool in combination withSHELXC/D/E for validation, MR-SAD and atom identification.
XPREP or SHELXC
ANODE• calculate anomalous density• generate peak list• averaged anomalous density
for each atom type
name_fa.hkl
name.pdb
name_fa.res
name.pha
name.lsa
Input and available options
The program is used with the command:
anode name [options]
reads name.ent or name.pdb and name_fa.hkl
If the data indices might be inconsistent with the PDB, thealternative orientation can be used by –i. For the space groupsP31, P32 and P3 four indexing options exist and should be chosenby a number.A maximum resolution for FA can be given with a cut-off (-d) orby dampening (-b) which seems superior in our tests.
Output and available options
ANODE calculates the density map by Fast Fourier Transform.
The square root of the density variance σ is derived.
Output:
• Averaged density for each site type, for example S_Met
• Heights and coordinates of unique peaks and distance to thenext atom in the PDB file.
• Map name.pha for COOT
• name_fa.res as written by SHELXD for usage with SHELXE
• name.lsa – listing file
Example 2: MAD
Data 3-WavelengthsInflection
pointPeak
High energy remote
Experiment MAD SAD SAD SAD
Zn2+ 82.5 55.7 66.4 56.0
Ca2+ (mean) 11.2 15.1 11.1 12.8
SD_Met (mean) 1.8 3.5 2.3 2.9
Unknown 28.5 18.2 24.7 20.1
Ratio Ca2+/Zn2+ 0.136 0.271 0.167 0.229
Ratio Unk./Zn2+ 0.345 0.326 0.372 0.359
Peak height over σ as given by ANODE
MR-SAD
input highest peak (σ) correct CC (SHELXE)
MR solution 4.713 12 6.66%
ARCIMBOLDO output 9.905 54 31.93%
final structure 12.273 60 32.10%
• The input PDB model can be a MR solution.
• Anomalous peaks can be used as substructure.
• Hence, MR-SAD can be done with ANODE.
This was tested for Hellethionin D:
Conclusion
• Effective and fast way to generate and analyseanomalous scatterers and heavy atoms
• Works well with weak signal
• Identification of atoms and structure validation
• Visualization of radiation damage to disulfides
• MR-SAD or validation of MR solutions
• Available at http://shelx.uni-ac.gwdg.de/SHELX
• The program ANODE is a standalone EXE file
• SHELXC or XPREP is needed to set up _fa.hkl files
ACKNOWLEDGEMENTS
ANODE was programmed by George M. Sheldrick.
The program was tested by Christian Große and Tobias Beck.
Test data were provided by Marianna Biadene, Gabor Buncoczi, JuditDebreczeni, Ina Dix, Tim Gruene, Uwe Müller and Manfred Weiss.
I also want to thank the Sheldrick group for the support in the last years!