摘要:

A survey of 129 protein crystal structures with more than one molecule per asymmetric unit shows that local (non‐crystallographic) symmetry axes are not randomly oriented. When compared to the crystal cell edges, face diagonals, body diagonal and reciprocal cell edges, 65% of the local symmetry axes are found to be parallel to one of the reference directions to within 15°; another 18% are orthogonal to within 3°; only 17% are in general orientations. In monoclinic, trigonal and hexagonal crystals, a majority of the local symmetry axes are orthogonal to the unique axis, while preferred orientations are parallel to the cell edges in orthorhombic cryst

ISSN:1399-0047    

DOI:10.1107/S0907444993003737

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The three‐dimensional crystal structure of recombinant bovine interferon‐γ was determined using the multiple isomorphous replacement method at 3.0 Å and refined to anRfactor of 19.2%. This protein crystallizes in space groupP212121with unit‐cell parameters ofa= 42.8,b= 79.9 andc= 85.4 Å. There is one functional dimer in the asymmetric unit. The two polypeptide chains are related by a non‐crystallographic twofold symmetry axis. The secondary structure is predominantly α‐helical with extensive interdigitation of the α‐helical segments of the polypeptide chains that make up the dimer. The secondary structure, tertiary structure and topology of this molecule are identical to the previously reported structures of recombinant rabbit interferon‐γ and recombinant human interferon‐γ. The molecular topology is also similar to that of murine interferon‐β. These structural similarities strongly indicate the presence of a unique topological feature (fold) among γ‐interferons from different species, and also among the

ISSN:1399-0047    

DOI:10.1107/S0907444993006924

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

A probability distribution of the structure factor is established from the analysis of the effects of errors involved in the multiple‐wavelength anomalous diffraction (MAD) method. This probability distribution, derived from those of the intensities, is two‐dimensional for acentric reflections and uni‐dimensional for centric reflections. It permits, using the centroid of the distribution, the calculation of the modulus and the phase of the `best' structure factor. The procedure for extracting the phase and its figure of merit is presented. Tests performed on simulated data show the contribution of this method with respect to other methods which use a distribution of only the phase as a function of the error of cl

ISSN:1399-0047    

DOI:10.1107/S0907444993007462

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

In judging the effectiveness of methods of solving crystal structures, or in phase refinement and development, two criteria are commonly used. The first is the mean phase error, which may be weighted in some way, and the second is the map correlation coefficient which describes the similarity of a map with estimated phases to that with true phases. It is shown that these two measures are directly related and that given the individual phase errors the map correlation coefficient may be found without the need to calculate a map. Various aspects of this connection are examined, including the map correlation coefficient when weights are used for calculating maps and the conditions under which phase extension leads to maps with a higher map correlation coefficient – which involves a balance between the advantage of employing more data and the disadvantage that the extra data may have a higher average phase erro

ISSN:1399-0047    

DOI:10.1107/S0907444993005852

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The X‐ray structures of native carboxypeptidase A and of the enzyme–inhibitor complex withl‐phenyl lactate have been refined at 1.54 and 1.45 Å resolution toRfactors of 0.151 and 0.161, respectively. Crystals of the complex were isomorphous with the native crystals (space groupP21,a= 51.60,b= 60.27,c= 47.25 Å, β = 97.27°). The high‐resolution electron density allowed correction of many side‐chain positions in the classical carboxypeptidase A model. This reflects the advantages of the high‐quality complete synchrotron data collected with an imaging plate detector. The conformational changes in the active centre of the enzyme upon binding of the inhibitor are restricted to only two residues, Tyr248 and Arg145.l‐Phenyl lactate is bound in the S1′ pocket and forms hydrogen bonds to Arg145, Glu270 and to the zinc‐bound water molecule. The present structure provides an explanation for the higher stability of the complexes with the products of esterolysis in comparison with those of amidolysis. This is consistent with the finding that product release is rate limiting for es

ISSN:1399-0047    

DOI:10.1107/S0907444993007267

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The X‐ray structure of the inhibitor complex of bovine ribonuclease A with cytidylic acid (2′‐CMP) has been determined at 1.6 Å resolution and refined by restrained least squares toR= 0.17 for 11 945 reflections. Binding of the inhibitor molecule to the protein is confirmed to be in the productive mode associated with enzyme activity. A study of conserved solvent sites amongst high‐resolution structures in the same crystal form reveals a stabilizing water cluster between the N a

ISSN:1399-0047    

DOI:10.1107/S090744499300719X

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The structure of an activated quaternary complex of ribulose 1,5‐bisphosphate carboxylase/oxygenase (rubisco) fromSynechococcusPCC6301 has been solved by molecular replacement. The protein crystallizes in an orthorhombicP212121unit cell with a complete L8S8complex consisting of 4608 residues (37 680 non‐hydrogen atoms) in the asymmetric unit. Data were collected both on film and image plate using synchrotron radiation; there were 218 276 unique reflections in the final 2.2 Å data set. The eightfold non‐crystallographic symmetry could be used both to improve map quality and to reduce the computing requirements of refinement. The coordinates were refined using strict non‐crystallographic symmetry constraints. The stereochemistry of the final model is good, and the model has anRvalue of 20.0% for the reflections betwe

ISSN:1399-0047    

DOI:10.1107/S090744499300530X

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The three‐dimensional structure of cadmium‐substituted concanavalin A has been refined usingX‐PLOR. TheRfactor on all data between 8 and 2 Å is 17.1%. The protein crystallizes in space groupI222 with cell dimensionsa= 88.7,b= 86.5 andc= 62.5 Å and has one protein subunit per asymmetric unit. The final structure contains 237 amino acids, two Cd ions, one Ca ion and 144 water molecules. One Cd ion occupies the transition‐metal binding site and the second occupies an additional site, the coordinates of which were first reported by Weinzierl&Kalb [FEBS Lett.(1971),18, 268–270]. The additional Cd ion is bound with distorted octahedral symmetry and bridges the cleft between the two monomers which form the conventional dimer of concanavalin A. This study provides a detailed analysis of the refined structure of saccharide‐free concanavalin A and is the basis for comparison with saccharide complexes r

ISSN:1399-0047    

DOI:10.1107/S0907444993006390

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The canine parvovirus (CPV) empty‐capsid structure has been determined and refined to 3.0 Å resolution in the tetragonal space groupP43212 with cell dimensionsa=b= 254.5 andc= 795.0 Å. The successful structure determination shows that reasonably good diffraction data were obtained in spite of the very longcaxis. The structure was solved by molecular replacement using the electron density of CPV full particles in a monoclinic space group. The phases were refined by non‐crystallographic symmetry averaging. The structure refinement was carried out by using the programsPROLSQandX‐PLOR. The finalRfactor for the structure that included 85 water molecules per icosahedral asymmetric unit was 21.1% for reflections between 6.0 and 3.0 Å resolution with an r.m.s. deviation of bond lengths of 0.020 Å from ideal values. The structure of CPV empty capsids showed conformational differences with respect to full capsids at a region where icosahedrally ordered DNA in full particles interacts with the capsid protein. It also confirmed the absence of density along the fivefold axis in the CPV empty‐particle structure in contrast to the situation in

ISSN:1399-0047    

DOI:10.1107/S0907444993006870

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

We have crystallized Nodamura virus, aT= 3 icosahedral virus that can infect both mammalian and insect hosts. Crystals are monoclinic, with two crystallographically independent virus molecules per asymmetric unit. Packing analysis reveals a pseudo‐rhombohedral (pseudo‐C2 in the monoclinic setting) arrangement of virus particles in the crystal lattice. Crystals differ from theR32 symmetry by rotational and translational deviations. The rhombohedral packing arrangement and its failure to describe the exact virus packing is analyzed in detail. The icosahedral threefold axis is rotated from the body diagonal of the pseudo‐rhombohedral cell, breaking the rhombohedral symmetry. TheC2 pseudo‐symmetry breaks down rotationally and/or translat

ISSN:1399-0047    

DOI:10.1107/S0907444993007498

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY