PMID:16421448

Citation	Mooers, BH and Matthews, BW (2006) Extension to 2268 atoms of direct methods in the ab initio determination of the unknown structure of bacteriophage P22 lysozyme. Acta Crystallogr. D Biol. Crystallogr. 62:165-76
Abstract	The X-ray crystal structure of the previously unknown bacteriophage P22 lysozyme, the product of gene 19, has been determined ab initio by direct methods using the program SIR2002. The presence of several partially occupied iodine anions and samarium cations augmented the ability of direct methods to locate all 2268 non-H protein atoms in the asymmetric unit, making this one of the largest structures to date to be determined ab initio. The iodides were introduced from a quick soak, which the crystal survived sufficiently well to diffract to 1.04 angstroms resolution. The complete heavy-atom substructure contributed 6.6% of the total scattering power. The initial determination of the structure assumed that there were two iodide ions in the asymmetric unit, although it was later determined that these sites correspond to partially occupied samarium ions. Tests suggested that it is better to overestimate rather than underestimate the heavy-atom content. While experimental phases from all of the successful tests were of high quality, the best results came from a SAD experiment using the programs SHELXD and SHELXE. Nonetheless, ab initio structure determination by direct methods was found to be a viable alternative to traditional protein crystallographic methods provided that the X-ray data extend to atomic resolution and heavy atoms with sufficient scattering power are present in the crystal.
Links	PubMed Online version:10.1107/S0907444905037212
Keywords	Bacteriophage P22/enzymology; Binding Sites; Crystallization; Crystallography, X-Ray; Iodides/chemistry; Iodides/metabolism; Models, Molecular; Molecular Structure; Muramidase/chemistry; Muramidase/genetics; Mutagenesis, Site-Directed; Protein Conformation; Samarium/chemistry; Samarium/metabolism
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
BPP22:ENLYS		GO:0003796: lysozyme activity	ECO:0000314:		F		Figure 6a shows a scatter plot diagram of electron-density map vs. the B factor in P22 lysozyme. The peak densities for N and O atoms decreases with the atomic temperature factor; the distribution of C atoms moves away from decay. Figure 6b shows C, N, and O decreasing very similarly exponentially.	complete CACAO 12916

References

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