Pf1 filamentous bacteriophage: refinement of a molecular model by simulated annealing using 3.3 Å resolution X-ray fibre diffraction data

1995 ◽  
Vol 51 (5) ◽  
pp. 792-804 ◽  
Author(s):  
A. Gonzalez ◽  
C. Nave ◽  
D. A. Marvin
Author(s):  
P.R. Smith ◽  
W.E. Fowler ◽  
U. Aebi

An understanding of the specific interactions of actin with regulatory proteins has been limited by the lack of information about the structure of the actin filament. Molecular actin has been studied in actin-DNase I complexes by single crystal X-ray analysis, to a resolution of about 0.6nm, and in the electron microscope where two dimensional actin sheets have been reconstructed to a maximum resolution of 1.5nm. While these studies have shown something of the structure of individual actin molecules, essential information about the orientation of actin in the filament is still unavailable.The work of Egelman & DeRosier has, however, suggested a method which could be used to provide an initial quantitative estimate of the orientation of actin within the filament. This method involves the quantitative comparison of computed diffraction data from single actin filaments with diffraction data derived from synthetic filaments constructed using the molecular model of actin as a building block. Their preliminary work was conducted using a model consisting of two juxtaposed spheres of equal size.


2002 ◽  
pp. 808-809 ◽  
Author(s):  
Mark Edgar ◽  
Vinton J. Carter ◽  
David P. Tunstall ◽  
Paramjit Grewal ◽  
Vincent Favre-Nicolin ◽  
...  

2010 ◽  
Vol 40 (3) ◽  
pp. 221-234 ◽  
Author(s):  
S. K. Straus ◽  
W. R. P. Scott ◽  
C. D. Schwieters ◽  
D. A. Marvin

Author(s):  
W. A. Crichton ◽  
G. B. M. Vaughan ◽  
M. Mezouar

AbstractThe structure of a 2-chain helical form of sulphur with 9 atoms per unit-cell has been determined from powder synchrotron x-ray diffraction data obtained at 3 GPa and 400ºC, using a combination of global optimization, simulated annealing and Rietveld refinement techniques. Final refinement of the structure in trigonal space group


2008 ◽  
Vol 41 (1) ◽  
pp. 56-61 ◽  
Author(s):  
Angela Altomare ◽  
Rocco Caliandro ◽  
Corrado Cuocci ◽  
Carmelo Giacovazzo ◽  
Anna Grazia Giuseppina Moliterni ◽  
...  

The solution of crystal structures from powder data using direct methods can be very difficult if the quality of the diffraction pattern is low and if no heavy atoms are present in the molecule. On the contrary, the use of direct-space methods does not require good quality diffraction data, but if a molecular model is available, the structure solution is limited principally by the number of degrees of freedom used to describe the model. The combination of the information contained in the electron density map (direct methods) with the Monte Carlo method, which uses simulated annealing as a global minimization algorithm (direct-space techniques), can be a useful tool for crystal structure solution, especially for organic structures. A modified and improved version of this approach [Altomareet al.(2003),J. Appl. Cryst.36, 230–238] has been implemented in theEXPO2004program and is described here.


2007 ◽  
Vol 40 (4) ◽  
pp. 702-709 ◽  
Author(s):  
Michela Brunelli ◽  
Marcus A. Neumann ◽  
Andrew N. Fitch ◽  
Asiloé J. Mora

The crystal structures of bicyclo[3.3.1]nonane-2,6-dione and bicyclo[3.3.1]nonane-3,7-dione have been solved by direct methods and by direct-space simulated annealing, respectively, from powder synchrotron X-ray diffraction data. Both compounds have a transition to a face-centred-cubic orientationally disordered phase (phase I) near 363 K, as shown by differential scanning calorimetry and powder diffraction measurements. Phase II of bicyclo[3.3.1]nonane-2,6-dione, which occurs below 363 K, is monoclinic, space groupC2/c, witha= 7.38042 (4),b= 10.38220 (5),c= 9.75092 (5) Å and β = 95.359 (1)° at 80 K. Phase II of bicyclo[3.3.1]nonane-3,7-dione, which occurs below 365 K, is tetragonal, space groupP41212, witha= 6.8558 (1) andc= 16.9375 (1) Å at 100 K. This phase coexists in a biphasic mixture with a minor monoclinic phase II′ [a= 11.450 (6),b = 20.583 (1),c= 6.3779 (3) Å, β = 94.7555 (5)°, at 100 K] detected in the sample, which impeded indexing with standard programs. The crystal structures of phases II were solved by direct methods and by direct-space simulated annealing, employing powder synchrotron X-ray diffraction data of increased instrumental intensity and resolution from the ID31 beamline at the ESRF, and novel indexing algorithms.Ab initiomolecular orbital calculations on the two systems are reported. In the solid state, the molecules pack in chair–chair conformation; molecular structures and packing are discussed.


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