On the solution of the molecular-replacement problem at very low resolution: application to large complexes

1995 ◽  
Vol 51 (6) ◽  
pp. 888-895 ◽  
Author(s):  
A. Urzhumtsev ◽  
A. Podjarny
Keyword(s):  
Molecular Replacement ◽  
Low Resolution ◽  
Replacement Problem

scholarly journals A global optimization method for the molecular replacement problem in X-ray crystallography

2005 ◽  
Vol 103 (2) ◽  
pp. 399-426
Author(s):  
Diane C. Jamrog ◽  
George N. Phillips Jr. ◽  
Richard A. Tapia ◽  
Yin Zhang
Keyword(s):  
Global Optimization ◽  
Optimization Method ◽  
Molecular Replacement ◽  
Global Optimization Method ◽  
X Ray ◽  
X Ray Crystallography ◽  
Replacement Problem

Molecular replacement with multiple different models

2004 ◽  
Vol 37 (1) ◽  
pp. 159-161 ◽  
Author(s):  
Nicholas M. Glykos ◽  
Michael Kokkinidis
Keyword(s):  
Crystal Structure ◽  
Original Description ◽  
Natural Generalization ◽  
Divide And Conquer ◽  
Search Model ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
Different Types ◽  
Replacement Problem ◽  
Special Case

Classical molecular replacement methods and the newer six-dimensional searches treat molecular replacement as a succession of sub-problems of reduced dimensionality. Due to their `divide-and-conquer' approach, these methods necessarily ignore (at least during their early stages) the very knowledge that a target crystal structure may comprise, for example, more than one copy of a search model, or several models of different types. An algorithm for a stochastic multi-dimensional molecular replacement search has been described previously and shown to locate solutions successfully, even in cases as complex as a 23-dimensional 4-body search. The original description of the method only dealt with a special case of molecular replacement, namely with the problem of placingncopies of only one search model in the asymmetric unit of a target crystal structure. Here a natural generalization of this algorithm is presented to deal with the full molecular replacement problem, that is, with the problem of determining the orientations and positions of a total ofncopies ofmdifferent models (withn≥m) which are assumed to be present in the asymmetric unit of a target crystal structure. The generality of this approach is illustrated through its successful application to a 17-dimensional 3-model problem involving one DNA and two protein molecules.

scholarly journals X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

2015 ◽  
Vol 10 (9) ◽  
pp. 1275-1284 ◽  
Author(s):  
Ryan N Jackson ◽  
Airlie J McCoy ◽  
Thomas C Terwilliger ◽  
Randy J Read ◽  
Blake Wiedenheft
Keyword(s):  
Electron Microscopy ◽  
Structure Determination ◽  
Molecular Replacement ◽  
Low Resolution ◽  
X Ray ◽  
Resolution Electron

Low-resolution molecular replacement using a six-dimensional search

2003 ◽  
Vol 59 (6) ◽  
pp. 1016-1019 ◽  
Author(s):  
Qun Liu ◽  
Arthur J. Weaver ◽  
Tao Xiang ◽  
Daniel J. Thiel ◽  
Quan Hao
Keyword(s):  
Molecular Replacement ◽  
Low Resolution

scholarly journals Crystallographic study of a MATE transporter presents a difficult case in structure determination with low-resolution, anisotropic data and crystal twinning

2015 ◽  
Vol 71 (11) ◽  
pp. 2287-2296 ◽  
Author(s):  
Jindrich Symersky ◽  
Yi Guo ◽  
Jimin Wang ◽  
Min Lu
Keyword(s):  
Structure Determination ◽  
Lessons Learned ◽  
Difficult Case ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Low Resolution ◽  
Membrane Transport Proteins ◽  
Crystal Twinning ◽  
Difference Fourier

NorM fromNeisseria gonorrhoeae(NorM-NG) belongs to the multidrug and toxic compound extrusion (MATE) family of membrane-transport proteins, which can extrude cytotoxic chemicals across cell membranes and confer multidrug resistance. Here, the structure determination of NorM-NG is described, which had been hampered by low resolution (∼4 Å), data anisotropy and pseudo-merohedral twinning. The crystal structure was solved using molecular replacement and was corroborated by conducting a difference Fourier analysis. The NorM-NG structure displays an extracellular-facing conformation, similar to that of NorM-NG bound to a crystallization chaperone. The approaches taken to determine the NorM-NG structure and the lessons learned from this study are discussed, which may be useful for analyzing X-ray diffraction data with similar shortcomings.

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