Biomedical subjects

Hongliang Xu

Publications and source records attributed to Hongliang Xu.

3 recordsLinked to original sources

PubMed2002

On integrating the techniques of direct methods and SIRAS: the probabilistic theory of doublets and its applications.

The mathematical formalism of direct methods is here applied to the SIRAS (single-isomorphous replacement combined with anomalous scattering) case. Specifically, the joint probability distribution of three structure factors, which plays the central role in the probabilistic theory of the two-phase structure invariants (doublets), is derived. This distribution leads directly to the conditional probability distribution of the two-phase structure invariants, given the values of selected sets of magnitudes. Furthermore, a probabilistic formula for estimating individual phases of the derivative structure is derived, provided that the heavy-atom substructure is assumed to be known. The formulas were tested for experimental SIRAS data and results are reported.

Acetylesterase↗

PubMed2002

Algebraic direct methods for few-atoms structure models.

As a basis for direct-methods phasing at very low resolution for macromolecular crystal structures, normalized structure-factor algebra is presented for few-atoms structure models with N = 1, 2, 3, em leader equal atoms or polyatomic globs per unit cell. Main results include: [see text]. Triplet discriminant Delta(hk) and triplet weight W(hk) parameters, a approximately 4.0 and b approximately 3.0, respectively, were determined empirically in numerical error analyses. Tests with phases calculated for few-atoms 'super-glob' models of the protein apo-D-glyceraldehyde-3-phosphate dehydrogenase (approximately 10000 non-H atoms) showed that low-resolution phases from the new few-atoms tangent formula were much better than conventional tangent formula phases for N = 2 and 3; phases from the two formulae were essentially the same for N > or = 4.

Crystallization↗

PubMed2001

Sine-enhanced Shake-and-Bake: the theoretical basis and applications to Se-atom substructures.

Shake-and-Bake is a dual-space direct-methods procedure for crystal structure determination capable of providing ab initio solutions for structures containing as many as 1200 independent non-H atoms, as well as for heavy-atom substructures containing as many as 160 Se atoms in the asymmetric unit. In traditional Shake-and-Bake, phase refinement in reciprocal space utilizes the technique of parameter shift to reduce the value of a minimal function that considers only the mean-square differences between the current values of the cosine structure invariants and their expected values. A new type of minimal function, termed the sine-enhanced minimal function, considers both cosine and sine values of the structure invariants. Exhaustive tests on six Se-atom substructures, ranging in size from 12 to 160 Se atoms in the asymmetric unit, have shown that a two- to eightfold increase in the percentage of trials that converge to solution is attainable with the technique of sine-enhanced parameter shift. The corresponding sine-enhanced Shake-and-Bake, with suitable default parameter values, is being incorporated into a new distributed version of the SnB computer program.

Crystallography, X-Ray↗