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Biomedical subjects

H F Fan

Publications and source records attributed to H F Fan.

11 recordsLinked to original sources
PubMed2004

Optimizing the error term in direct-method SAD phasing.

The probability formula of the direct-method SAD (single-wavelength anomalous diffraction) phasing proposed by Fan & Gu (1985, Acta Cryst. A41, 280-284) contains an error term which is related to the lack-of-closure error. This error term is used as a weighting function in the phase derivation and in the subsequent calculation of electron-density maps. Previously, there has been a constant in the error term that has had to be determined empirically for each particular case. It has been found that improper choice of the constant often leads to failure of the direct-method SAD phasing. The problem is resolved by introducing a modified error term and a method of automatically tuning the associated scaling factor.

Algorithms↗
PubMed2004

Direct-method SAD phasing with partial-structure iteration: towards automation.

The probability formula of direct-method SAD (single-wavelength anomalous diffraction) phasing proposed by Fan & Gu (1985, Acta Cryst. A41, 280-284) contains partial-structure information in the form of a Sim-weighting term. Previously, only the substructure of anomalous scatterers has been included in this term. In the case that the subsequent density modification and model building yields only structure fragments, which do not straightforwardly lead to the complete solution, the partial structure can be fed back into the Sim-weighting term of the probability formula in order to strengthen its phasing power and to benefit the subsequent automatic model building. The procedure has been tested with experimental SAD data from two known proteins with copper and sulfur as the anomalous scatterers.

Automation↗
PubMed2004

SAD phasing by combination of direct methods with the SOLVE/RESOLVE procedure.

In the initial stage of SAD phasing, the essential point is to break the intrinsic phase ambiguity. The presence of two kinds of phase information enables the discrimination of phase doublets from SAD data prior to density modification. One is from the heavy atoms (anomalous scatterers), while the other is from the direct-methods phase relationships. The former can be expressed by the Sim distribution, while the latter can be expressed by the Cochran distribution. Typically, only the Sim distribution has been used to yield initial phases for subsequent density modification. However, it has been demonstrated that using direct-methods phases based on the product of the Sim and Cochran distributions can lead to improved initial phases. In this paper, the direct-methods phasing procedure OASIS has been improved and combined with the SOLVE/RESOLVE procedure. Experimental SAD data from three known proteins with expected Bijvoet ratios / in the range 1.4-7.0% were used as test cases. In all cases, the phases obtained using the program RESOLVE beginning with initial phases based on experimental phases plus Sim and direct-methods information were more accurate than those based on experimental plus Sim phase information alone.

Azurin↗
PubMed2002

Direct-method-aided phasing of MIR diffraction data from proteins.

Direct methods have successfully been used to break the phase ambiguity intrinsic in the single isomorphous replacement (SIR) data of proteins. Based on this, the procedure 'direct-method-aided MIR phasing' (DMIR) has been proposed and applied to the four-derivative multiple isomorphous replacement (MIR) data of a known protein containing 682 amino acid residuals in the asymmetric unit. The data set consists of 14,500 unique reflections at 3 A resolution with F(obs.) greater than 2sigma. Test calculation showed that the phases from conventional MIR phasing could be significantly improved by direct methods leading to obvious improvement in the quality of the resultant Fourier maps.

Crystallography, X-Ray↗
PubMed2001

Electron crystallographic image-processing investigation and superstructure determination for (Pb0.5Sr0.3Cu0.2)Sr2(Ca0.6Sr0.4)Cu2Oy.

An electron crystallographic image-processing technique based on the combination of high-resolution electron microscopy and electron diffraction has been developed to investigate the commensurate structural modulation in the high-Tc superconductor (Pb0.5Sr0.3Cu0.2)Sr2(Ca0.6Sr0.4)Cu2Oy. After symmetry averaging, a structure image was obtained by image deconvolution at the resolution limited by that of the electron microscope. Then phase extension was employed to enhance the image resolution up to about 1.25 A by means of the electron diffraction data corrected with an empirical method. In the final projected potential map, the occupational and/or positional modulation is clearly observed for all atoms, including oxygen. The key points of determining superstructures by the technique are studied and discussed.

Journal Article↗
PubMed2001

Direct-method-aided phasing of MAD data.

The direct methods of breaking the phase ambiguity intrinsic in one-wavelength anomalous scattering (OAS) data and MAD phasing are powerful methods in their own rights. In a different context, in addition to their success in phasing OAS data, direct methods can also be useful in the treatment of MAD data. The idea has been tested with the MAD data at 2.5 A resolution from the protein human adenosine kinase [Mathews et al. (1998), Biochemistry, 37, 15607--15620]. The results showed that the incorporation of direct methods in MAD phasing led to a significant improvement of phases over those obtained from the conventional MAD phasing method alone, as indicated by improved map correlation coefficients (with the existing model), reduced phase errors by 4.5 degrees and improved map connectivity.

Adenosine Kinase↗
PubMed1999

Combining direct methods with isomorphous replacement or anomalous scattering data. VIII. Phasing experimental SIR data with the replacing atoms in a centrosymmetric arrangement.

A multisolution direct method has been proposed to resolve the phase ambiguity intrinsic in single isomorphous replacement data of proteins with the replacing atoms in a centrosymmetric arrangement. The phase ambiguity of each reflection is in fact a 'sign ambiguity' of the phase difference between the phase of the native protein and that of the replacing atoms, i.e. +/- |Deltatheta| = theta - theta'. The P+ probability formula can be used to derive the signs. The multisolution phasing procedure is initiated using random starting values of P+. A cluster analysis is used instead of figures of merit to find the correct solution. The direct-method phases can be further improved by density-modification techniques. The method was tested with the experimental SIR data at 2 A resolution from a known protein aPP; satisfactory results were obtained.

Animals↗
PubMed1997

Use of single isomorphous replacement data of proteins - resolving the phase ambiguity and a new procedure for phase extension.

A procedure combining direct methods and solvent flattening to break the phase ambiguity intrinsic to the single isomorphous replacement (SIR) technique has been tested with the experimental SIR data of the known protein RNase Sa at 2.5 A resolution. The use of direct methods provided better initial phases for the solvent-flattening procedure, while the solvent-flattening procedure greatly improved direct-method phases leading to a traceable Fourier map. A small subset of known phases at low resolution makes direct phasing of SIR data much easier. Accordingly a method for extending low-resolution phases to high-resolution ones is proposed making use of additional SIR information. This reduces the problem of finding a value in the range of 0-2pi for each unknown phase to that of just making a choice between two possible values. Tests with the known protein RNase Sa showed that the method is able to extend phases from a resolution of 6 to 2.5 A leading to an easily traceable Fourier map. The solvent-flattening technique and the combination of which with direct methods were used for the phase extension. Either procedure yielded reasonably good results, but on the whole, the result from the combination of direct methods with solvent flattening is better. Results of the latter procedure were further compared with that from direct phasing of the 2.5 A SIR data and with that from phase extension by solvent flattening without SIR information. An improvement gained by the use of SIR information is evident.

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↗
PubMed1986

Loss of propranolol during ultrafiltration in plasma protein binding studies.

A commercial ultrafiltration device was examined for propranolol plasma protein binding studies. A nonspecific loss of free drug resulted in a low recovery in the ultrafiltrate. Use of a rinse filtrate did not completely compensate for this loss. Use of different centrifugal forces indicated the loss was not due to significant membrane rejection of drug. Equilibrating the device with sample for four hours slightly improved the recovery while use of a higher ionic strength buffer had no effect. Propranolol was bound by the membrane, but there was a larger, continuous loss to the o-ring. Results with an alternate commercial device were also unsatisfactory.

Blood Proteins↗