scholarly journals HAD, a Data Bank of Heavy-Atom Binding Sites in Protein Crystals: a Resource for Use in Multiple Isomorphous Replacement and Anomalous Scattering

1998 ◽  
Vol 54 (6) ◽  
pp. 1199-1206 ◽  
Author(s):  
Suhail A. Islam ◽  
David Carvin ◽  
Michael J. E. Sternberg ◽  
Tom L. Blundell
Keyword(s):  
Binding Sites ◽  
Heavy Atom ◽  
Data Bank ◽  
Protein Crystals ◽  
Anomalous Scattering ◽  
Isomorphous Replacement ◽  
Crystallization Conditions ◽  
Derivatives Of ◽  
Coordinate Data

Information on the preparation and characterization of heavy-atom derivatives of protein crystals has been collected, either from the literature or directly from protein crystallographers, and assembled in the form of a heavy-atom data bank (HAD). The data bank contains coordinate data for the heavy-atom positions in a form that is compatible with the crystallographic data in the Brookhaven Protein Data Bank, together with a wealth of information on the crystallization conditions, the nature of the heavy-atom reagent and references to relevant publications. Some statistical information derived from the data bank, such as the most popular heavy-atom derivatives, is also included. The information can be directly accessed and should be useful to protein crystallographers seeking to improve their success in preparing heavy-atom derivatives for the methods of isomorphous replacement and anomalous dispersion. The World Wide Web address of HAD is http://www.icnet.uk/bmm/had.

Freeze-Trapping Isomorphous Xenon Derivatives of Protein Crystals

1997 ◽  
Vol 30 (4) ◽  
pp. 476-486 ◽  
Author(s):  
O. Sauer ◽  
A. Schmidt ◽  
C. Kratky
Keyword(s):  
Heavy Atom ◽  
Sperm Whale ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Anomalous Scattering ◽  
Isomorphous Replacement ◽  
Potential Applications ◽  
Xenon Pressure ◽  
Gas Consumption ◽  
Derivatives Of

A simple and efficient method to prepare isomorphous derivatives of protein crystals with xenon as a heavy atom is described. The method consists of exposing a crystal to xenon gas of pressures above 5 atm (~ 0.5 MPa) for several minutes and subsequently shock-freezing the crystal to immobilize the xenon dissolved in the mother liquor and bound to the protein. Diffraction data can the be collected with the established techniques of protein cryocrystallography. Two types of high-pressure device are described to expose a protein crystal to the required xenon pressure, permitting rapid freeze-quenching after xenon exposure. One of these devices can be used for gas pressures up to and exceeding 5.0 MPa, with a gas consumption of a few millilitres of uncompressed gas. The technique has been tested with monoclinic crystals of sperm-whale metmyoglobin, which has four xenon binding sites. The results of these experiments are described and discussed. Potential applications of this technique include-besides the classical multiwavelength anomalous diffraction (MAD) or single isomorphous replacement with anomalous scattering (SIRAS) experiments-the derivation of low-angle phase information by modifying the electron density of the solvent regions within the crystal.

scholarly journals ANODE: anomalous and heavy-atom density calculation

2011 ◽  
Vol 44 (6) ◽  
pp. 1285-1287 ◽  
Author(s):  
Andrea Thorn ◽  
George M. Sheldrick
Keyword(s):  
Phase Shift ◽  
Heavy Atom ◽  
Data Bank ◽  
Protein Data Bank File ◽  
Anomalous Scattering ◽  
Atom Density ◽  
Usual Procedure ◽  
Isomorphous Replacement ◽  
Multiple Wavelength ◽  
Potential Applications

The new programANODEestimates anomalous or heavy-atom density by reversing the usual procedure for experimental phase determination by methods such as single- and multiple-wavelength anomalous diffraction and single isomorphous replacement anomalous scattering. Instead of adding a phase shift to the heavy-atom phases to obtain a starting value for the native protein phase, this phase shift is subtracted from the native phase to obtain the heavy-atom substructure phase. The required native phase is calculated from the information in a Protein Data Bank file of the structure. The resulting density enables even very weak anomalous scatterers such as sulfur to be located. Potential applications include the identification of unknown atoms and the validation of molecular replacement solutions.

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.

Membrane's Eleven: heavy-atom derivatives of membrane-protein crystals

2006 ◽  
Vol 62 (8) ◽  
pp. 877-882 ◽  
Author(s):  
J. Preben Morth ◽  
Thomas Lykke-Møller Sørensen ◽  
Poul Nissen
Keyword(s):  
Membrane Protein ◽  
Heavy Atom ◽  
Protein Crystals ◽  
Derivatives Of

In-house characterization of protein powder

2010 ◽  
Vol 43 (4) ◽  
pp. 876-882 ◽  
Author(s):  
Christian Grundahl Hartmann ◽  
Ole Faurskov Nielsen ◽  
Kenny Ståhl ◽  
Pernille Harris
Keyword(s):  
Powder Diffraction ◽  
Data Bank ◽  
Lorentz Factor ◽  
Cell Parameters ◽  
Geometric Factors ◽  
Diffraction Patterns ◽  
A Minor ◽  
Coordinate Data ◽  
Good Agreement

X-ray powder diffraction patterns of lysozyme and insulin were recorded on a standard in-house powder diffractometer. The experimental powder diffraction patterns were compared with patterns calculated from Protein Data Bank coordinate data. Good agreement was obtained by including straightforward corrections for background, unit-cell parameters, disordered bulk solvent and geometric factors. In particular the solvent correction was found crucial for a good agreement. A revised Lorentz factor was derived, which gave a minor, but significant, improvement to the fit in the low-angle region. An attempt to include calculated H-atom positions did not improve the overall fit and was abandoned. The method devised was shown to be a quick and convenient tool for distinguishing precipitates and polymorphs of proteins.

IL MILIONE: a suite of computer programs for crystal structure solution of proteins

2007 ◽  
Vol 40 (3) ◽  
pp. 609-613 ◽  
Author(s):  
Maria C. Burla ◽  
Rocco Caliandro ◽  
Mercedes Camalli ◽  
Benedetta Carrozzini ◽  
Giovanni L. Cascarano ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Electron Density ◽  
Heavy Atom ◽  
Direct Methods ◽  
Computer Programs ◽  
Atomic Resolution ◽  
Protein Crystal ◽  
Anomalous Scattering ◽  
Isomorphous Replacement ◽  
Phase Extension

IL MILIONEis a suite of computer programs devoted to protein crystal structure determination by X-ray crystallography. It may be used in the following key activities. (a)Ab initiophasing,viaPatterson or direct methods. The program may succeed even with structures with up to 6000 non-H atoms in the asymmetric unit, provided that atomic resolution is available, and with data at quasi-atomic resolution (1.4–1.5 Å). (b) Single or multiple isomorphous replacement, single- or multiple-wavelength anomalous diffraction, and single or multiple isomorphous replacement with anomalous scattering techniques. In the first step the program finds the heavy-atom/anomalous scatterer substructure, then automatically uses the above information to phase protein reflections. Phase extension and refinement are performed by electron density modification techniques. (c) Molecular replacement. The orientation and the location of the protein molecules are foundviareciprocal space methods. Phase extension and refinement are performed by electron density modification techniques. All the programs integrated intoIL MILIONEare controlled by means of a user-friendly graphical user interface, which is used to input data and to monitor intermediate and final results by means of real-time updated messages, diagrams and histograms.

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