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J X Yao

Publications and source records attributed to J X Yao.

12 recordsLinked to original sources
PubMed2006

ACORN: a review.

The ACORN system was originally developed as a means of ab initio solution of protein structures when atomic resolution data were available. The first step is to obtain a starting set of phases, which must be at least slightly better than random. These may be calculated from a fragment of the structure, which can be anything from a single metal atom to a complete molecular-replacement model. A number of standard procedures are available in ACORN to orientate and position such a fragment. The fragment provides initial phases that give the first of a series of maps that are iteratively refined by a dynamic density-modification (DDM) process. Another FFT-based procedure is Sayre-equation refinement (SER), which modifies phases better to satisfy the Sayre equation. With good-quality atomic resolution data, the final outcome of applying DDM and SER is a map similar in appearance to that found from a refined structure, which is readily interpreted by automated procedures. Further development of ACORN now enables structures to be solved with less than atomic resolution data. A critical part of this development is the artificial extension of the data from the observed limit to 1 A resolution. These extended reflections are allocated unit normalized structure amplitudes and then treated in a similar way to observed reflections except that they are down-weighted in the calculation of maps. ACORN maps, especially at low resolution, tend to show C atoms less well, in particular C(alpha) atoms which fall within the first diffraction minimum of their three neighbours. Two new density-modification procedures (DDM1 and DDM2) and a density-enhancement procedure (ENH) have been devised to counter this problem. It is demonstrated that high-quality maps showing individual atoms can be produced with the new ACORN. ACORN has also been demonstrated to be very effective in refining phase sets derived from physical processes such as those using anomalous scattering or isomorphous derivative data. Future work will be directed towards applying ACORN to resolutions down to 2 A.

Computer Simulation↗
PubMed1996

Direct-space methods in phase extension and phase refinement. V. The histogram moments method.

Any distribution is completely defined by its moments. It is shown that a process of phase refinement can be carried out, based on Fourier transforms, which modifies the moments of electron density, separately in the protein and solvent regions, towards target values. Tests have been carried out on two moderate-sized proteins with 800-900 atoms in the asymmetric unit, one containing heavy atoms and the other not. It has been found that refinement using the third moment about zero in the protein region is most effective and that refinement with higher moments, or in the solvent region, adds nothing useful. Two kinds of weights are necessary in the method. One is for giving a weighted mixture of new phase indications with original phase estimates from, say, multiple isomorphous replacement. The other weights are applied to the Fourier coefficients of density maps to give the best possible signal:noise ratio. These weights have been explored empirically and the best ones found are described. It is concluded that since the moments method, which changes phases in reciprocal space, is independent of other histogram-matching procedures, which change density in real space, it has something to offer in a refinement package containing several procedures.

Journal Article↗
PubMed1995

Direct phasing of one-wavelength anomalous-scattering data of the protein core streptavidin.

The direct method [Fan, Hao, Gu, Qian, Zheng & Ke (1990). Acta Cryst. A46, 935-939] was used to break the phase ambiguity intrinsic to one-wavelength anomalous scattering data from a known protein of moderate size, core streptavidin, which was solved originally with three-wavelength anomalous diffraction data [Hendrickson, Pähler, Smith, Satow, Merritt & Phizackerley (1989). Proc. Natl Acad. Sci. USA, 86, 2190-2194]. Unlike that in the previous test with a small protein, the Fourier map calculated with the direct-method phases could not clearly reveal the moderate-sized protein structure. However, the phases can be improved step by step using Wang's solvent-flattening method, non-crystallographic symmetry averaging and the skeletonization method. The final electron-density map clearly shows most Calpha positions and some side chains and it is traceable without prior knowledge of the structure. It is concluded that the direct method is capable of breaking the OAS phase ambiguity of a moderate-sized protein at moderate resolution such as 3 A, while the combination of direct methods with macromolecular techniques may produce phases good enough for unknown protein structure to be traced.

Journal Article↗
PubMed1994

On the application of one-wavelength anomalous scattering. IV. The absolute configuration of the anomalous scatterers.

An essential first step in most techniques for using anomalous-scattering data for phase determination is to determine the positions of the anomalous scatterers. This is usually done by use of the anomalous differences, either as input to a direct-methods procedure or to produce a Patterson map. If the arrangement of anomalous scatterers is noncentrosymmetric then it is also necessary to find their absolute configuration and a process is described for doing this based on the properties of the P(s) function [Okaya, Saito & Pepinsky (1955). Phys. Rev. 98, 1857-1858]. If the arrangement of anomalous scatterers is centrosymmetric then the problem does not occur.

Journal Article↗
PubMed1993

[The characters on histopathological changes in dental fluorosis]

The microradiography SEM and TEM were used ton observe histopathological changes in dental fluorasis with various degrees in this study.The characters of histopathological changes of dental fluorasis are:(1) the lesios appear in exterior layer of enamel,not excess one third enamel.(2)the future of the lesion is enamel-hypoplasia,enamel rods were hypomineralized.the space among enamel rods widen and form some cavities.There are a lot of spaces in intercrystlines.Many micropores and injures exhibit on enamel surface.(3)the clinic severe degree of lesion is similar to the histopathological changes.It could be indicated using the Dean's and the TF index.

Journal Article↗
PubMed1987

Structure determination of kanglemeisu A by X-ray diffraction method.

Kanglemeisu A (C50H63O19B.CH3OH) is the product of an actinomyces species from a soil sample gathered in China Kanglemeisu A belongs to the triclinic system, space group P1, unit cell: a = 12.760(3), b = 10.287(2), c = 9.926(2) A, alpha = 88.39(2), beta = 78.64(2), gamma = 89.14(2). RANTAN direct method is used to solve the structure. The final discrepancy factor is R = 0.0689, after atom coordinates and temperature factors have been refined with full matrix least squares. The structure skeleton consists of four parts, the naphthalene nucleus connected to the 5-membered ring, a 17-membered ring connected to C2, a dimethyl butane diacid extended out from C20, beta-D-3,4-OO' methylenedigitoxose passing through an oxygen bridge O6 and linked to C27 of ansa ring.

Anti-Bacterial Agents↗
PubMed1985

Intrafascicular decompression in the treatment of causalgia with special reference to the mechanism.

A new concept of the pathogenesis of causalgia is suggested in accordance with experimental and clinical work. Endoneural hypertension secondary to nerve trunk disruption is incriminated and intrafascicular decompression is used as the key therapeutic measure. In 14 patients with causalgia thus treated, all except 1 were cured. No symptomatic recurrence was noted in a 4- to 6-year follow-up study.

Adolescent↗
PubMed1985

Free musculocutaneous flap transfer of extensor digitorum brevis muscle by microvascular anastomosis for restoration of function of thenar and adductor pollicis muscles.

This article reports 3 cases of surgical restoration of function of the thenar muscle and the adductor pollicis muscle of the thumb with free musculocutaneous flaps of the extensor digitorum brevis muscle of the toe by microsurgical technique. Two years' follow-up revealed good functional recovery of the hand with normal electromyographic findings and grade 3-4 muscular power.

Adolescent↗