1. Score maps improve clarity of density maps
Dusan Turk
Dept. Biochemistry and Mol. and Struct. Biology, Jozef Stefan Insitute
Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins

2. Computational parts of macromolecular crystallography
- diffraction data processing and evaluation,
- phasing (isomorphous or molecular replacement),
+ density modification (solvent flattening, averaging, ...)
+ model building or density interpretation
+ refinement,
+ structure validation,
+ figure preparation,
- paper writing
MAIN software for density averaging, model building, structure refinement and validation
Acta Crystallographica Section D (August 2013)
Biological Crystallography ISSN

3. Clarity of maps is crucial for the macromolecular structure interpretation.
Initial electron density maps are often rather noisy:
- Map improvements:
- Density modification,
- Correction terms (bulk, anisotropic, ...)
- Density averaging,
- Maximum likelihood scaling,
- Averaged kicked maps,
- B-value sharpening,
- ….
- Score maps as a density modification.

4. Solvent flattening
Solvent flattening
Assessment of molecule envelope by averaging of positive density density within a sphere. Sphere corresponding to the size of molecules.
Molecular envelope border is assigned on histogram of scored map corresponding to the level of volume occupied by the molecule.
Wang, B.C. (1985) Resolution of phase ambiguity in macromolecular crystallography. Methods in Enzymology 115,
Leslie, A. (1987) A reciprocal-space method for calculating a molecular envelope using the algorithm of B.C. Wang. Acta Cryst. A43,

5. The whole range of score map
Contours
The whole range of score map
12A sphere: Score map contour from 50% solvent to 92%
Reduction of sphere radius from 12A to 1.4A

6. 2.6A MAD Cytochrome C oxidase
solvent flattened map
Score map using 2.6A sphere
Soulimane, T., Buse, G., Bourenkov, G. P., Bartunik, H. D., Huber, R. & Than, M. E. (2000). EMBO J 19,

7. Standard maps ML / averaged
Molecular replacement 2.2A data, cathepsin V – clitocypin complex inhibitor
Initial ML 2Fobs – Fmodel map phasing with cathepsin V only
Averaged initial map
Renko M, Sabotic J, Mihelic M, Brzin J, Kos J, Turk D.(2010). J Biol Chem. 285,

8. Score map from averaged map Build model
Fixed cathepsin V, increasing envelope
Score map from averaged map
Build model

9. Score map from averaged map
Refining cathepsin V with NCS using envelope of built model
Score map from averaged map
Built model

10. Stefin I4 / I422, 1.8A resolution
order – rotational disorder structure
Two overlaying tetrameric formations
Score maps of partial omit Fobs – Fmodel maps
Renko et al., unpublished

11. Each 5th layer is rotationally disordered

12. Summary Any kind of map can be scored by a sphere
- heavy atom phasing,
- density modification including density averaging,
- model based 2Fobs-Fmodel and Fobs-Fmodel.
In the sphere radius dependent manner visualization of structural features becomes clearer and easier (for manual and automated map interpretation):
- helices (5-7A)
- chain trace (3-4)
- side chain positioning (2-3.5)
- alternative positions / conformations

13. Acknowledgments
MAIN users who contributed to development of this idea over the last years
Chairs of the session
Jouise Dawe
Jason Mercer
Group member
Miha Renko
Resources
Structural Biology Grant,
ARRS