[10] Electron-density map interpretation

1997 ◽  
pp. 173-208 ◽  
Author(s):  
T.A. Jones ◽  
M. Kjeldgaard
Keyword(s):  
Electron Density ◽  
Map Interpretation ◽  
Density Map ◽  
Electron Density Map

Refinement of Netropsin Bound to DNA: Bias and Feedback in Electron Density Map Interpretation

Biochemistry ◽  
1995 ◽  
Vol 34 (15) ◽  
pp. 4983-4993 ◽  
Author(s):  
David S. Goodsell ◽  
Mary L. Kopka ◽  
Richard E. Dickerson
Keyword(s):  
Electron Density ◽  
Map Interpretation ◽  
Density Map ◽  
Electron Density Map

Errors and reproducibility in electron-density map interpretation

1999 ◽  
Vol 55 (7) ◽  
pp. 1309-1319 ◽  
Author(s):  
Sherry L. Mowbray ◽  
Charlotte Helgstrand ◽  
Jill A. Sigrell ◽  
Alexander D. Cameron ◽  
T. Alwyn Jones
Keyword(s):  
Escherichia Coli ◽  
Electron Density ◽  
Main Chain ◽  
Real Space ◽  
Side Chain ◽  
Map Interpretation ◽  
Quality Check ◽  
Density Map ◽  
Electron Density Map

Three investigators, with varying levels of experience, independently built and refined the structure of Escherichia coli ribokinase at 2.6 Å resolution. At the end of the refinement/rebuilding processes the models had essentially converged, although each had its own particular pattern of remaining errors. The subsequent refinement of the same structure at 1.8 Å resolution allowed an overall quality check of each of the lower resolution models, and an analysis of which graphics-based tools were generally most efficient in locating these errors. Criteria which are useful in the application of Ramachandran, main-chain and side-chain database and real-space fit analyses are presented.

A Comparison of Two Algorithms for Electron-Density Map Improvement by Introduction of Atomicity: Skeletonization, and Map Sorting Followed by Refinement

1998 ◽  
Vol 54 (1) ◽  
pp. 81-85 ◽  
Author(s):  
F. M. D. Vellieux
Keyword(s):  
Electron Density ◽  
Initial Density ◽  
Acta Cryst ◽  
Density Maps ◽  
Resolution Electron ◽  
Crystallographic Symmetry ◽  
Density Map ◽  
Ornithine Transcarbamoylase ◽  
Electron Density Map ◽  
Pseudo Atom

A comparison has been made of two methods for electron-density map improvement by the introduction of atomicity, namely the iterative skeletonization procedure of the CCP4 program DM [Cowtan & Main (1993). Acta Cryst. D49, 148–157] and the pseudo-atom introduction followed by the refinement protocol in the program suite DEMON/ANGEL [Vellieux, Hunt, Roy & Read (1995). J. Appl. Cryst. 28, 347–351]. Tests carried out using the 3.0 Å resolution electron density resulting from iterative 12-fold non-crystallographic symmetry averaging and solvent flattening for the Pseudomonas aeruginosa ornithine transcarbamoylase [Villeret, Tricot, Stalon & Dideberg (1995). Proc. Natl Acad. Sci. USA, 92, 10762–10766] indicate that pseudo-atom introduction followed by refinement performs much better than iterative skeletonization: with the former method, a phase improvement of 15.3° is obtained with respect to the initial density modification phases. With iterative skeletonization a phase degradation of 0.4° is obtained. Consequently, the electron-density maps obtained using pseudo-atom phases or pseudo-atom phases combined with density-modification phases are much easier to interpret. These tests also show that for ornithine transcarbamoylase, where 12-fold non-crystallographic symmetry is present in the P1 crystals, G-function coupling leads to the simultaneous decrease of the conventional R factor and of the free R factor, a phenomenon which is not observed when non-crystallographic symmetry is absent from the crystal. The method is far less effective in such a case, and the results obtained suggest that the map sorting followed by refinement stage should be by-passed to obtain interpretable electron-density distributions.

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