摘要:

The low‐density elimination method for phase extension and refinement [Shiono&Woolfson (1992).Acta Cryst. A48, 451456] has been improved by substituting a smoother density‐modification procedure for the original sharp cut‐off function. In addition, better criteria have been found for limiting the number of refinement cycles, which gives a better final result for much less work. The effectiveness of the process has been illustrated by phase refinement for a protein with high‐resolution (1.17 Å) data containing 808 independent non‐H atoms plus 83 water molecules in the asymmetric unit; the unweighted mean‐phase error was reduced from 74 to 39.3°. Phase extension and refinement was also demonstrated for pig 2Zn insulin starting with multiple isomorphous replacement (MIR) phases at 1.9 Å and extending out to 1.5 Å. There was a significant improvement of phases and the final map had a correlation

ISSN:1399-0047    

DOI:10.1107/S0907444993003282

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

C‐1027‐AG, the apoprotein of the macromolecular antitumor antibiotic C‐ 1027, isolated fromStreptomyces globisporus, was crystallized by the vapor‐diffusion procedure using 2‐methyl‐2,4‐pentanediol as a precipitant. The crystals belong to the orthorhombic system, space groupP212121, with unit‐cell dimensionsa= 55.1,b= 61.3 andc= 79.1 Å. Assuming that the asymmetric unit contains two or three molecules, theVmvalue is calculated as 3.2 or 2.1 Å3 Da−1, respectively. A total of 7630 independent reflections was obtained up to 2.5 Å resolution with synchrotron radiation, the mergingRfactor being 0

ISSN:1399-0047    

DOI:10.1107/S0907444993002719

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The structure determination of a macromolecule from a hemihedrally twinned crystal specimen with a twinning fraction of one‐half is described. Twinning was detected by analysis of crystal‐packing density and intensity statistics. The structure was solved using molecular replacement, and the positioned search model was used to overcome the twinning by a novel method of `detwinning' the observed data. Estimates of the unobservable crystallographic intensities from each of the twin domains were obtained and used to refine the model. The structure of a new algal plastocyanin fromChlamydomonas reinhardtiiwas determined by this method to 1.6 Å resolution with a `twinned'Rfactor of 15.6%. Additional data from a crystal specimen with a low twinning fraction were used to establish the accuracy of the structure solution from the perfectly twinned data, and to finalize the refinement to 1.5 Å resolution and a trueRfactor of 16.8%. Methods for detecting twinning and obtaining a molecular‐replacement solution in the presence of twinning ar

ISSN:1399-0047    

DOI:10.1107/S090744499300294X

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The crystal structure of a binary complex of the porcine heart catalytic (C) subunit of cAMP‐dependent protein kinase (space groupP4132;a= 171.5 Å) complexed with a di‐iodinated peptide inhibitor, PKI(5–24), has been solved and refined to 2.9 Å resolution with an overallRof 21.1%. The r.m.s. deviations from ideal bond lengths and angles are 0.022 Å and 4.3°. A single isotropicBof 17 Å2was used for all atoms. The structure solution was carried out initially by molecular replacement of electron density followed by refinement against atomic coordinates from orthorhombic crystals of a binary complex of the mouse recombinant enzyme previously described [Knighton, Zheng, Ten Eyck, Ashford, Xuong, Taylor&Sowadski (1991).Science,253, 407–414]. The most striking difference between the two crystal structures is a large displacement of the small lobe of the enzyme. In the cubic crystal, the β‐sheet of the small lobe is rotated by 15° and translated by 1.9 Å with respect to the orthorhombic crystal. Possible explanations for why this binary complex crystallized in an open conformation in contrast to a similar binary complex of the recombinant enzyme are discussed. This study demonstrates that considerable information about parts of a crystal structure can be obtained without a complete crystal structure analysis. Specifically, the six rigid‐group parameters of a poly alanine model of the β‐structure were obtained satisfactorily from a crystal structure by refinement of difference Fourier coefficients based on an app

ISSN:1399-0047    

DOI:10.1107/S0907444993002306

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The crystal structure of bovine seminal ribonuclease, a homodimeric enzyme closely related to pancreatic ribonuclease, has been refined at a nominal resolution of 1.9 Å employing data collected on an electronic area detector. The final model consists of two chains containing 1990 non‐H atoms, seven sulfate anions and 113 water molecules per asymmetric unit. The unit‐cell parameters area= 36.5 (1),b= 66.7 (1) andc= 107.5 (2) Å, space groupP22121. TheRfactor is 0.177 for 16 492 reflections in the resolution range 6.0–1.9 Å and the deviations from ideal values of bond lengths and bond angles are 0.020 Å and 3.7°, respectively. The molecule is formed by two pancreatic like chains, which have their N‐terminal segments interchanged so that each active site is formed by residues from both subunits. The two chains are related by a non‐crystallographic twofold symmetry and are covalently linked by two consecutive disulfide bridges, which form an unusual sixteen‐membered ring across the dimer interface. The deviations from the molecular symmetry, the hydration shell and the sulfate‐binding sites are also discussed in relation to the known

ISSN:1399-0047    

DOI:10.1107/S0907444993003403

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The structure of triosephosphate isomerase (TIM) from the organismEscherichia colihas been determined at a resolution of 2.6 Å. The structure was solved by the molecular replacement method, first at 2.8 Å resolution with a crystal grown by the technique of hanging‐drop crystallization from a mother liquor containing the transition‐state analogue 2‐phosphoglycolate (2PG). As a search model in the molecular replacement calculations, the refined structure of TIM fromTrypanosoma brucei, which has a sequence identity of 46% compared to the enzyme fromE. coli, was used. AnE. coliTIM crystal grown in the absence of 2PG, diffracting to 2.6 Å resolution, was later obtained by application of the technique of macro‐seeding using a seed crystal grown from a mother liquor without 2PG. The final 2.6 Å model has a crystallographicRfactor of 11.9%, and agrees well with standard stereochemical parameters. The structure ofE. coliTIM suggests the importance of residues which favour helix initiation for the formation of the TIM fold. In addition, TIM fromE. colishows peculiarities in its dimer interface, and in the packing of core residues

ISSN:1399-0047    

DOI:10.1107/S0907444993002628

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

Crystals of domainAofThermus flavus5S rRNA have been obtained. The space group was found to beP43with unit‐cell dimensionsa=b= 30.10 andc= 86.80 Å. Data to 2.3 Å have been recorded and solution of the structure is currently underway by means of molecular‐replacement t

ISSN:1399-0047    

DOI:10.1107/S0907444993001520

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

The OP‐G2 monoclonal antibody binds to the platelet integrin, gpIIb/IIIa, in a mode that mimics fibrinogen binding. The specificity of this antibody is mediated by the third complementarity‐determining region (CDR3) loop of the immunoglobulin heavy chain which contains a sequence (RYD) related to the RGD recognition sequence of fibrinogen. The OP‐G2 Fab fragment has been crystallized by vapor diffusion from solutions containing polyethylene glycol and imidazole malate (pH 5.6). The crystals belong to space groupP21212 witha= 93.1,b= 83.8 andc= 53.7 Å. One Fab molecule is present in the asymmetric unit. A complete data set to 2.0 Å resolution has be

ISSN:1399-0047    

DOI:10.1107/S0907444993002501

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

摘要:

. An active recombinant preparation of the carboxy‐terminal ribonuclease H (RNase H) domain of HIV‐I reverse transcriptase has produced crystals of several different forms, including a trigonal prism form (P31;a=b= 52.03,c= 113.9 Å with two molecules per asymmetric unit) and a hexagonal tablet form (P6222 orP6422;a=b= 93.5,c= 74.1 Å with one molecule per asymmetric unit). The former appears to be isomorphous with crystals of a similar, but inactive, version of the enzyme that was used for a prior crystal structure determination [Davies, Hostomska, Hostomsky, Jordan&Matthews (1991).Science,252, 88–95]. We have also obtained a structure solution for this crystal form and have refined it with 2.8 Å resolution data (R= 0.216). We report here details of our crystallization studies and some initial structural results that verify that the preparation of active HIV‐1 RNase H yields a protein that is not just enzymatically, but also structurally, distinguishable from the inactive form. Evidence suggests that region 538–542, which may be involved in the catalytic site and which is disordered in both molecules in the prior structure determination, is ordered in the crystal structure of the active enzyme, although the ordering may include more than one conformation for this loop. It should also be noted that, in the crystal structure of the trigonal form, RNase H monomers associate to form noncrystallographic twofold‐symmetric dimers by fusing five‐stranded mixed β sheets into a single ten‐stranded dimerwide sheet, an assembly that was not remarked upon

ISSN:1399-0047    

DOI:10.1107/S0907444993002409

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY

ISSN:1399-0047    

DOI:10.1107/S0907444993099731

出版商:International Union of Crystallography    

年代:1993

数据来源: WILEY