Ab initio phase determination for X-ray diffraction data from crystals of a native protein

Ab initio phasing starting from low resolution

A single set of structure factor magnitudes complete at low resolution plus information of a general type are sufficient to get initial phases for macromolecular crystals which allow one to see the molecular packing and an approximate envelope. Followed by a more careful analysis based on the same information, these ab initio phases can be extended so that the corresponding maps show secondary structure elements.

Ca1-xNa2xAl2B2O7: A Structure with Tunable Density of Na+ Vacancies

A series of samples with the composition Ca(1)(-)(x)Na(2)(x)Al(2)B(2)O(7) (0 < x < or = 1) was investigated and a hexagonal structure with unusually large range of homogeneity (at least from x = 0.01 to 0.95) was revealed. The hexagonal phase consists of [Al(2)B(2)O(7)](infinity)(2)(-) lamellae stacked along the c axis, as in CaAl(2)B(2)O(7) and Na(2)Al(2)B(2)O(7). Nevertheless, the configuration and stacking sequence of the [Al(2)B(2)O(7)](infinity)(2)(-) lamellae are different in these three structures. In the hexagonal structure of Ca(1)(-)(x)()Na(2)(x)()Al(2)B(2)O(7), Ca and half Na cations (Na1) statistically occupy the same crystallographic site which is located between the [Al(2)B(2)O(7)](infinity)(2)(-) lamellae, the other half Na cations (Na2) distribute in the planes bisecting the [Al(2)B(2)O(7)](infinity)(2)(-) lamellae. Depending on the composition, the site occupation factor of Na2 site can vary in the same range as x, leading to a tunable density of Na(+) vacancies in the structure. The AlO(4) tetrahedra and BO(3) triangles in the structure tilt in appropriate ways to improve the bond valence sum of Na2 cations which are not sufficiently bonded to the anions.

Determination of protein and solvent volumes in protein crystals from contrast variation data

By varying the relative values of protein and solvent scattering densities in a crystal, it is possible to obtain information on the shape and dimensions of protein molecular envelopes. Neutron diffraction methods are ideally suited to these contrast variation experiments because H/D exchange leads to large differential changes in the protein and solvent scattering densities and is structurally non-perturbing. Low resolution structure factors have been measured from cubic insulin crystals with differing H/D contents. Structure factors calculated from a simple binary density model, in which uniform scattering densities represent the protein and solvent volumes in the crystals, were compared with these data. The contrast variation differences in the sets of measured structure factors were found to be accurately fitted by this simple model. Trial applications to two problems in crystal structure determination illustrate how this fact may be exploited. (i) A translation function that employs contrast variation data gave a sharp minimum within 1-9A of the correctly positioned insulin molecule and is relatively insensitive to errors in the atomic model. (ii) An ab initio phasing method for the contrast variation data, based on analyzing histograms of the density distributions in trial maps, was found to recover the correct molecular envelope.

Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy

Macromolecular structure determination by X-ray crystallography and solution NMR spectroscopy has experienced unprecedented growth during the past decade.