scholarly journals Direct Phasing of Protein Crystals with Non-Crystallographic Symmetry

Crystals ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 55
Author(s):  
Hongxing He ◽  
Mengchao Jiang ◽  
Wu-Pei Su
Keyword(s):  
Ab Initio ◽  
Diffraction Data ◽  
Model Building ◽  
Projection Algorithm ◽  
Protein Crystals ◽  
Translation Vector ◽  
Solvent Content ◽  
Crystallographic Symmetry ◽  
Automatic Model Building ◽  
Molecular Envelope

An iterative projection algorithm proposed previously for direct phasing of high-solvent-content protein crystals is extended to include non-crystallographic symmetry (NCS) averaging. For proper NCS, when the NCS axis is positioned, the molecular envelope can be automatically rebuilt. For improper NCS, when the NCS axis and the translation vector are known, the molecular envelope can also be automatically reconstructed. Some structures with a solvent content of around 50% could be directly solved using this ab initio phasing method. Trial calculations are described to illustrate the methodology. Real diffraction data are used and the calculated phases are good for automatic model building. The refinement of approximate NCS parameters is discussed.

FINDNCS: a program to detect non-crystallographic symmetries in protein crystals from heavy-atom sites

1999 ◽  
Vol 32 (2) ◽  
pp. 365-368 ◽  
Author(s):  
Guoguang Lu
Keyword(s):  
Protein Data Bank ◽  
Root Mean Square ◽  
Heavy Atom ◽  
Data Bank ◽  
Protein Crystals ◽  
Translation Vector ◽  
Mean Square ◽  
Acta Cryst ◽  
Crystallographic Symmetry ◽  
Averaging Techniques

In order to facilitate applications of averaging techniques in the MIR/MAD procedure, a program,FINDNCS, which automatically identifies non-crystallographic symmetry (NCS) from heavy-atom sites, has been developed. The program outputs the NCS operations (a rotation matrix and a translation vector), the corresponding root-mean-square (r.m.s.) deviations of heavy-atom sites, polar angles and screw translations, and writes coordinates of matching sites in Protein Data Bank (PDB) format. The program has an interface with the graphics programO[Joneset al. (1991).Acta Cryst.A47, 110–119] so that the NCS operations can be displayed automatically. In the test examples, all the correct NCS operations were identified and were above the noise solutions.

Direct phasing of protein crystals with high solvent content

2015 ◽  
Vol 71 (1) ◽  
pp. 92-98 ◽  
Author(s):  
Hongxing He ◽  
Wu-Pei Su
Keyword(s):  
Weighted Average ◽  
Protein Crystals ◽  
Average Error ◽  
Transform Method ◽  
High Resolution Data ◽  
Solvent Content ◽  
Crystallographic Symmetry ◽  
Density Map ◽  
Average Electron ◽  
Electron Density Map

An iterative transform method is proposed for solving the phase problem in protein crystallography. In each iteration, a weighted average electron-density map is constructed to define an estimated protein mask. Solvent flattening is then imposed through the hybrid input–output algorithm [Fienup (1982).Appl. Opt.21, 2758–2769]. Starting from random initial phases, after thousands of iterations the mask evolves into the correct shape and the phases converge to the correct values with an average error of 30–40° for high-resolution data for several protein crystals with high solvent content. With the use of non-crystallographic symmetry, the method could potentially be extended to phase protein crystals with less than 50% solvent fraction. The new phasing algorithm can supplement and enhance the traditional refinement tools.

Iterative projection algorithms in protein crystallography. II. Application

2015 ◽  
Vol 71 (4) ◽  
pp. 451-459 ◽  
Author(s):  
Victor L. Lo ◽  
Richard L. Kingston ◽  
Rick P. Millane
Keyword(s):  
Model Building ◽  
Protein Crystallography ◽  
Structural Redundancy ◽  
Convergence Properties ◽  
Projection Algorithms ◽  
Electron Densities ◽  
Promising Tool ◽  
Crystallographic Symmetry ◽  
Crystallographic Axes ◽  
Molecular Envelope

Iterative projection algorithms (IPAs) are a promising tool for protein crystallographic phase determination. Although related to traditional density-modification algorithms, IPAs have better convergence properties, and, as a result, can effectively overcome the phase problem given modest levels of structural redundancy. This is illustrated by applying IPAs to determine the electron densities of two protein crystals with fourfold non-crystallographic symmetry, starting with only the experimental diffraction amplitudes, a low-resolution molecular envelope and the position of the non-crystallographic axes. The algorithm returns electron densities that are sufficiently accurate for model building, allowing automated recovery of the known structures. This study indicates that IPAs should find routine application in protein crystallography, being capable of reconstructing electron densities starting with very little initial phase information.

Solvent content of protein crystals

1968 ◽  
Vol 33 (2) ◽  
pp. 491-497 ◽  
Author(s):  
B.W. Matthews
Keyword(s):  
Protein Crystals ◽  
Solvent Content
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