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Resolve examples

Removal of model bias with prime-and-switch phasing

IF5A molecular replacement phasing

Dehalogenase molecular replacement phasing

Improvement of experimentally- phased maps

IF5A MAD map

Removal of model bias with prime-and-switch phasing

IF5A molecular replacement phasing

The system: initiation factor 5A (IF5A)
X-ray data on P. aerophilum IF5A to 2.2 A (Peat T.S., Newman J, Waldo G.S, Berendzen J. & Terwilliger T.C. Structure Of Translation Initiation-Factor 5a From Pyrobaculum aerophilum At 1.75 Angstrom Resolution. Structure 6, 1207-1214 (1998))
60% solvent
atomic model from M. jannaschii IF5A (Kim, K. K, Hung, L. W., Yokota, H., Kim, R. & Kim, S.-H. Crystal structures of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 angstrom resolution. Proc. Natl. Acad Sci. USA 95, 10419-10424 (1998))
RMSD between atomic model from M. jannaschii and refined P. aerophilum structure is 1.7 A.
The test: phase the P. aerophilum data with the M. jannaschii structure
Methods tested: (a) sigma-A, (b) prime-and-switch, (c) omit map, and (d) density modification (with resolve)
Results: (MR model in blue, correct model in yellow). Sigma-A map looks a lot like the model in blue used to calculate it; prime-and-switch map looks just like the correct model in yellow. Omit map is noisy, and density-modified map is halfway between sigmaA and prime-and-switch.

Removal of model bias with prime-and-switch phasing

Dehalogenase molecular replacement phasing

The system: Rhodococcus dehalogenase (dhlA)
X-ray data on Rhodococcus dhlA to 1.5 A (Newman, J., Peat, T. S., Richard, R., Kan, L., Swanson, P. E., Affholter, J. A., Holmes, I. H., Schindler, J. F., Unkefer, C. J., & Terwilliger, T. C. Haloalkane dehalogenases: Structure of a Rhodococcus enzyme. Biochemistry 38, 16105-16114 (1999).)
30% solvent
atomic model from dehalogenase linB from S. paucimobilis(Marek, J., Vevodova, J., Smatanova, I. K., Nagata, Y., Svensson, L. A., Newman, J., Takagi, M. & Damborsky, J. Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. Biochemistry 39, 14082-14086 (2000).)
RMSD between atomic model from S. paucimobilis lin B and refined RhodococcusdhlA structure is 1.4 A.
The test: phase the Rhodococcus dhlA data with the S. paucimobilis linB structure
Methods tested: (a) sigma-A, (b) prime-and-switch, (c) omit map, and (d) density modification (with resolve)
Results: (MR model structure is in blue, correct model in yellow). SigmaA map looks like the MR model used to calculate it; prime-and-switch map looks like the correct model.

Improvement of experimentally-phased maps
IF5A MAD map

(See: Peat, T. S., Newman, J., Waldo, G. S., Berendzen, J. & Terwilliger, T. C. (1998) "Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 A resolution" Structure 15, 1207-1214.

MAD dataset on initiation factor 5A
Only 1 of 3 selenium atoms in 147 residues used in phasing (just for this test example)
Solvent content was 60%
Resolution of 2 A, space group I4
Initial correlation of experimental map with one based on refined model was 0.37
Correlation after resolve was 0.79
Correlation after conventional solvent flattening and histogram matching (using dm) was 0.65

Initial MAD map (CC=0.37)

Resolve map (CC=0.79)

Conventional solvent flattening & histogram matching (CC=0.65)