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

Acta Crystallogr D Biol Crystallogr

Hauptman-Woodward Medical Research Institute and Department of Structural Biology, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 73 HighStreet, Buffalo, NY 14203 USA.

Published: January 2002

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.

Download full-text PDF

Source
http://dx.doi.org/10.1107/s0907444901017668DOI Listing

Publication Analysis

Top Keywords

minimal function
12
sine-enhanced shake-and-bake
8
se-atom substructures
8
160 atoms
8
atoms asymmetric
8
asymmetric unit
8
parameter shift
8
function considers
8
structure invariants
8
sine-enhanced
4

Similar Publications

Patient-Initiated Brief Admission (PIBA) is perceived as a constructive intervention. It remains uncertain whether PIBA contributes to healthier behaviors among its users. To comprehend patients' motivation to engage in health-promoting behaviors, it is essential to understand how various nursing interventions influence the behavior-specific thoughts and feelings that lead to healthy behaviors.

View Article and Find Full Text PDF

The global dental implant market is projected to reach $9.5 billion by 2032, growing at a 6.5% compound annual growth rate due to the rising prevalence of dental diseases.

View Article and Find Full Text PDF

Efflux pumps that transport antibacterial drugs out of bacterial cells have broad specificity, commonly leading to broad spectrum resistance and limiting treatment strategies for infections. It remains unclear how efflux pumps can maintain this broad spectrum specificity to diverse drug molecules while limiting the efflux of other cytoplasmic content. We have investigated the origins of this broad specificity using theoretical models informed by the experimentally determined structural and kinetic properties of efflux pumps.

View Article and Find Full Text PDF

Bacterial cytokinesis begins with polymerization of the tubulin homologue FtsZ into a ring-like structure at midcell, the Z-ring, which recruits the late cell division proteins that synthesize the division septum. Assembly of FtsZ is carefully regulated and supported by a dozen conserved cell division proteins. Generally, these proteins are not essential, but removing more than one is in many cases lethal.

View Article and Find Full Text PDF

This study examined the effects of treadmill running (TR) regimens on craniofacial pain- and anxiety-like behaviors, as well as their effects on neural changes in specific brain regions of male mice subjected to repeated social defeat stress (SDS) for 10 days. Behavioral and immunohistochemical experiments were conducted to evaluate the impact of TR regimens on SDS-related those behaviors, as well as epigenetic and neural activity markers in the anterior cingulate cortex (ACC), insular cortex (IC), rostral ventromedial medulla (RVM), and cervical spinal dorsal horn (C2). Behavioral responses were quantified using multiple tests, while immunohistochemistry measured histone H3 acetylation, histone deacetylases (HDAC1, HDAC2), and neural activity markers (FosB and phosphorylated cAMP response element-binding protein (pCREB).

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!