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12644298622
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note
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Monomeric αHL was isolated from cell culture supernatants of Staphylococcus aureus (Wood strain 46; ATCC 10832). Assembly was catalyzed by deoxycholate (9); and the heptamer was purified to homogeneity (as judged from SDS-PAGE, gel filtration, and analytical velocity and equilibrium ultracentrifugation data) by size exclusion chromatography in the presence of 40 mM n-octyl-β-glucoside.
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12644253787
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note
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3 were obtained after 2 to 4 weeks. Diffraction data were collected with the use of CuKα x-rays at room temperature and either an Enraf-Nonius FAST or a Rigaku R-Axis IIc area detector system. Integrated intensities were obtained from the FAST data by means of MADNES and PROCOR (29) and ROTAVATA/AGROVATA (30), and from the R-Axis data with the Rigaku PROCESS software. All data sets listed above were collected on the FAST system except for the native data set II which was collected on the R-Axis. For the native data set II, three crystals were used. The strongest data from the three crystals were merged and reprocessed to generate the final ∼14-fold redundant native data set.
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31
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12644303179
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note
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6 and soaked for 1 to 2 weeks. The major uranyl and osmium sites were determined by inspection of difference Patterson maps. Difference Fourier maps were used to locate minor sites and sites in other derivatives. Heavy atom positions were refined with XHeavy in the XtalView package (32) and phases were calculated with the program PHASES (33). A MIR electron density map was calculated at 3.0 Å resolution from which a protein-solvent boundary could be discerned as well as prominent elements of secondary structure. Density modification which included solvent flattening, histogram matching, and noncrystallographic symmetry averaging by means of the program DM (37) improved the quality of the electron density map. DM was also used for phase extension from 3.0 to 2.4 Å and from 3.0 Å to 1.9 Å with the FAST and R-Axis IIc data sets, respectively.
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38
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12644253788
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note
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Initial structures for a protomer were independently built into the 2.4 Å map with Xfit (32) and Bones-Lego-O (39). Both models yielded the same trace and similar side chain positions. The six additional protomers were obtained by application of the noncrystallographic symmetry (NCS) transformations followed by manual readjustments, first in the 2.4 Å map and then in the 1.9 Å map.
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30 (G) were replaced by alanine (A). Analysis of the structure by PROCHECK (57) indicates that all residues occupy allowed regions of the Ramachandran plot.
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44
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0001339532
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Figures were created from the following programs. MOLSCRIPT: P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); RASTER3D: E. A. Merritt, M. E. P. Murphy, Acta Crystallogr. D50, 869 (1994); XtalView (32); GRASP: A. Nicholls, K. A. Sharp, B. Honig, Proteins: Struct. Funct. Genet. 11, 281 (1991): SETOR: S. V. Evans, J. Mol. Graphics, 11, 134 (1993).
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Figures were created from the following programs. MOLSCRIPT: P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); RASTER3D: E. A. Merritt, M. E. P. Murphy, Acta Crystallogr. D50, 869 (1994); XtalView (32); GRASP: A. Nicholls, K. A. Sharp, B. Honig, Proteins: Struct. Funct. Genet. 11, 281 (1991): SETOR: S. V. Evans, J. Mol. Graphics, 11, 134 (1993).
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Figures were created from the following programs. MOLSCRIPT: P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991); RASTER3D: E. A. Merritt, M. E. P. Murphy, Acta Crystallogr. D50, 869 (1994); XtalView (32); GRASP: A. Nicholls, K. A. Sharp, B. Honig, Proteins: Struct. Funct. Genet. 11, 281 (1991): SETOR: S. V. Evans, J. Mol. Graphics, 11, 134 (1993).
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12644271842
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note
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We thank a balciurias for crystallization assistance, K. Cowtan P. Lox, B, Perman, D. Picot, B. Ramachandran, Z. Ben, X.-J. Yang, and members of tne Bayley, Souaux, Garavito, and Moffat groups for assistance and comments: and H.-M. Ke (U. of North Carolina) for area detector time and helpful suggestions Supported in part by funds from a PHS/NIH Shared instrumentation Grant and a Louis Block grant, respectively, for the FAST and R-Axis IIo area detectors. initial refinement was performed at the Pittsburgh Supercomputer Center. This work was supported in part by grants from the Office of Naval Research (J.E.G. and H.B.), the NIH (J.E.G.), the;Martin D and Virginia S, Kamen Sustaining Fund for junior faculty (J.E.G), the Searle Sohoiars Program (J.E.G.), the NSF (J.E.G.), and the DOE (H.B.), the Cancer Research Foundation Young investigator fund (J.E.G.), and the Medical Scientist Training Program at the University of Chicago (M.R.H.). The coordinates have been deposited at the Protein Data Bank at Brookhaven with accession number 7ahl.
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