“The training of a crystallographer frequently reminds me ...shelx.uni-ac.gwdg.de/~athorn/pdf/thorn_iucr2011_anode.pdf · “The training of a crystallographer frequently reminds

“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)

ANODE: ANOmalous and heavy atom DEnsity

Andrea Thorn

August 26th, 2011

Software Fayre IUCR Madrid

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 1: Viscotoxin B2

Example 2: MAD

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

Radiation damage

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!