A Translation-Function Approach for Heavy-Atom Location in Macromolecular Crystallography

1998 ◽  
Vol 54 (3) ◽  
pp. 400-402 ◽  
Author(s):  
Alexei Vagin ◽  
Alexei Teplyakov
Keyword(s):  
Heavy Atom ◽  
Unit Cell ◽  
Function Approach ◽  
Macromolecular Crystallography ◽  
Heavy Atoms ◽  
Anomalous Data ◽  
Translation Function ◽  
Full Symmetry

A method for locating heavy atoms in the unit cell of macromolecular crystals by a full-symmetry translation function is described. The approach has been implemented in the program TRAHALO and tested on experimental isomorphous and anomalous data.

scholarly journals Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methods

1999 ◽  
Vol 55 (2) ◽  
pp. 501-505 ◽  
Author(s):  
Thomas C. Terwilliger ◽  
Joel Berendzen
Keyword(s):  
Electron Density ◽  
Heavy Atom ◽  
Density Variation ◽  
Low Density ◽  
Macromolecular Crystallography ◽  
Anomalous Data ◽  
Density Maps

An automated examination of the native Fourier is tested as a means of evaluation of a heavy-atom solution in MAD and MIR methods for macromolecular crystallography. It is found that the presence of distinct regions of high and low density variation in electron-density maps is a good indicator of the correctness of a heavy-atom solution in the MIR and MAD methods. The method can be used to evaluate heavy-atom solutions during MAD and MIR structure solutions and to determine the handedness of the structure if anomalous data have been measured.

A Base Specific Single Heavy Atom Stain for Electron Microscopy

1972 ◽  
Vol 30 ◽  
pp. 184-185
Author(s):  
J. P. Langmore ◽  
N. R. Cozzarelli ◽  
A. V. Crewe
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
High Resolution ◽  
Elastic Scattering ◽  
Heavy Atom ◽  
High Vacuum ◽  
Heavy Atoms ◽  
Large Movement ◽  
Base Sequencing ◽  
Scanning Electron

A system has been developed to allow highly specific derivatization of the thymine bases of DNA with mercurial compounds wich should be visible in the high resolution scanning electron microscope. Three problems must be completely solved before this staining system will be useful for base sequencing by electron microscopy: 1) the staining must be shown to be highly specific for one base, 2) the stained DNA must remain intact in a high vacuum on a thin support film suitable for microscopy, 3) the arrangement of heavy atoms on the DNA must be determined by the elastic scattering of electrons in the microscope without loss or large movement of heavy atoms.

Determination of the structure of bis(propyldithiocarbamate)nickel(II)

1990 ◽  
Vol 55 (4) ◽  
pp. 1010-1014 ◽  
Author(s):  
Jiří Kameníček ◽  
Richard Pastorek ◽  
František Březina ◽  
Bohumil Kratochvíl ◽  
Zdeněk Trávníček
Keyword(s):  
Molecular Structure ◽  
Title Compound ◽  
Crystal And Molecular Structure ◽  
Heavy Atom ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Planar Configuration ◽  
Compound C ◽  
Heavy Atom Method

The crystal and molecular structure of the title compound (C8H16N2NiS4) was solved by the heavy atom method and the structure was refined anisotropically to a final R factor of R = 0.029 (wR = 0.037) for 715 observed reflections. The crystal is monoclinic, space group P21/c with a = 948.3(2), b = 776.9(2), c = 1 167.4(2) pm, β = 125.14(2)°, Z = 2. The molecule contains two four-membered NiSCS rings of approximately planar configuration with the Ni atom situated at a centre of symmetry. The molecules are arranged in chains along the c-axis of the unit cell.

The crystal structure of myoglobin. VI. Seal myoglobin

1960 ◽  
Vol 258 (1293) ◽  
pp. 181-201 ◽  
Keyword(s):  
Tertiary Structure ◽  
Heavy Atom ◽  
Three Dimensional ◽  
Sperm Whale ◽  
Fourier Synthesis ◽  
Heavy Atoms ◽  
Isomorphous Replacement ◽  
Unit Cells ◽  
The Common ◽  
Sperm Whale Myoglobin

Myoglobin from the common seal ( Phoca vitulina ) when crystallized from ammonium sulphate forms monoclinic crystals with space group the unit cell, a = 57·9Å, b = 29·6Å, c = 106·4Å, β = 102°15', contains four molecules. The method of isomorphous replacement has been used in an investigation of the centrosymmetric b -axis projection in which it has been possible to determine signs for nearly all the h0l reflexions having spacings greater than 4Å. Three independent heavy-atom derivatives were employed and the signs so determined have been used to compute a map of the electron density projected on the (010) plane. This projection has been interpreted in terms of the molecule of sperm-whale myoglobin, as deduced by Bodo, Dintzis, Kendrew & Wyckoff (1959) from a three-dimensional Fourier synthesis to 6Å resolution. The results of the interpretation show that the two myoglobin molecules are very similar in form (tertiary structure) in spite of the differences in their amino-acid composition. The relative orientation of the two unit cells with respect to the myoglobin molecule is given and a comparison is made of the positions of the heavy atoms in each molecule.

scholarly journals The magic triangle goes MAD: experimental phasing with a bromine derivative

2010 ◽  
Vol 66 (4) ◽  
pp. 374-380 ◽  
Author(s):  
Tobias Beck ◽  
Tim Gruene ◽  
George M. Sheldrick
Keyword(s):  
Functional Groups ◽  
Heavy Atom ◽  
Anomalous Dispersion ◽  
Proteinase K ◽  
Nonspecific Binding ◽  
Heavy Atoms ◽  
Carboxylate Groups ◽  
Experimental Phasing ◽  
Sad Phasing ◽  
Bromine Derivative

Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2,4,6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups and one amino group) that interact with proteinsviahydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br Kedge was successfully carried out. Radiation damage to the bromine–carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out.

scholarly journals Combining solution wide-angle X-ray scattering and crystallography: determination of molecular envelope and heavy-atom sites

2009 ◽  
Vol 42 (2) ◽  
pp. 259-264 ◽  
Author(s):  
Xinguo Hong ◽  
Quan Hao
Keyword(s):  
Structure Determination ◽  
Heavy Atom ◽  
Unit Cell ◽  
Wide Angle ◽  
X Ray ◽  
X Ray Scattering ◽  
Molecular Envelope ◽  
Waxs Data ◽  
Ray Scattering

Solving the phase problem remains central to crystallographic structure determination. A six-dimensional search method of molecular replacement (FSEARCH) can be used to locate a low-resolution molecular envelope determined from small-angle X-ray scattering (SAXS) within the crystallographic unit cell. This method has now been applied using the higher-resolution envelope provided by combining SAXS and WAXS (wide-angle X-ray scattering) data. The method was tested on horse hemoglobin, using the most probable model selected from a set of a dozen bead models constructed from SAXS/WAXS data using the programGASBORat 5 Å resolution (qmax= 1.25 Å−1) to phase a set of single-crystal diffraction data. It was found that inclusion of WAXS data is essential for correctly locating the molecular envelope in the crystal unit cell, as well as for locating heavy-atom sites. An anomalous difference map was calculated using phases out to 8 Å resolution from the correctly positioned envelope; four distinct peaks at the 3.2σ level were identified, which agree well with the four iron sites of the known structure (Protein Data Bank code 1ns9). In contrast, no peaks could be found close to the iron sites if the molecular envelope was constructed using the data from SAXS alone (qmax= 0.25 Å−1). The initial phases can be used as a starting point for a variety of phase-extension techniques, successful application of which will result in complete phasing of a crystallographic data set and determination of the internal structure of a macromolecule to atomic resolution. It is anticipated that the combination ofFSEARCHand WAXS techniques will facilitate the initial structure determination of proteins and provide a good foundation for further structure refinement.

Completion of crystal structures from powder data: the use of the coordination polyhedra

2000 ◽  
Vol 33 (6) ◽  
pp. 1305-1310 ◽  
Author(s):  
Angela Altomare ◽  
Carmelo Giacovazzo ◽  
Antonietta Guagliardi ◽  
Anna Grazia Giuseppina Moliterni ◽  
Rosanna Rizzi
Keyword(s):  
Structural Model ◽  
Heavy Atom ◽  
Computing Time ◽  
Direct Methods ◽  
Coordination Polyhedra ◽  
Trial Solution ◽  
Final Model ◽  
Heavy Atoms ◽  
Experimental Diffraction Pattern ◽  
User Intervention

Direct methods applied to powder diffraction data often provide well located heavy atoms and unreliable light-atom positions. The completion of the crystal structure is then not always straightforward and may require a considerable amount of user intervention. The heavy-atom connectivity provided by the trial solution may be used to guess the nature of the coordination polyhedra. A Monte Carlo procedure is described which, in the absence of a well defined structural model, is able to locate the light atoms correctly under the restraints of the experimental heavy-atom connectivity model. The correctness of the final model is assessed by criteria based on the agreement between the whole experimental diffraction pattern and the calculated one. The procedure requires little CPU computing time and has been implemented as a routine ofEXPO[Altomareet al.(1999).J. Appl. Cryst.32, 339–340]. The method has proved to be sufficiently robust against the distortion of the coordination polyhedra and has been successfully applied to some test structures.

scholarly journals Heavy atom effects in the Paternò–Büchi reaction of pyrimidine derivatives with 4,4’-disubstituted benzophenones

2011 ◽  
Vol 7 ◽  
pp. 113-118 ◽  
Author(s):  
Feng-Feng Kong ◽  
Jian-Bo Wang ◽  
Qin-Hua Song
Keyword(s):  
Temperature Effects ◽  
Halogen Atom ◽  
Heavy Atom ◽  
Photochemical Efficiency ◽  
Pyrimidine Derivatives ◽  
Heavy Atoms ◽  
Electron Withdrawing Group ◽  
Photochemical Systems ◽  
Expected Increase ◽  
Atom Effect

The regioselectivity and the photochemical efficiency were investigated in the Paternò–Büchi reaction of 1,3-dimethylthymine (DMT) and 1,3-dimethyluracil (DMU) with benzophenone (1b) and some 4,4’-disubstituted derivatives (dimethoxy (1a), difluoro (1c), dichloro (1d), dibromo (1e) and dicyano benzophenone (1f)) that gives rise to two regioisomeric oxetanes, 2 and 3. The regioselectivity (the ratio of 2/3) decreased gradually for both DMT/DMU photochemical systems from 1a to 1f. That is, a halogen atom as an electron-withdrawing group (EWG) has a pronounced effect on the regioselectivity. However, the photochemical efficiency of the 1e systems did not show the expected increase, but decreased relative to systems with 1b. Temperature effects on the regioselectivity of 1b–e systems showed some interesting features for systems with heavy atoms (including the 1d and 1e systems), such as higher inversion temperatures, and an entropy-controlled regioselectively whereas the regioselectivity for two other systems (1b and 1c) is enthalpy–entropy controlled. A heavy atom effect is suggested to be responsible for these unusual phenomena based on the triplet-diradical mechanism of the Paternò–Büchi reaction.

scholarly journals An overview of heavy-atom derivatization of protein crystals

2016 ◽  
Vol 72 (3) ◽  
pp. 303-318 ◽  
Author(s):  
Ashley C. W. Pike ◽  
Elspeth F. Garman ◽  
Tobias Krojer ◽  
Frank von Delft ◽  
Elisabeth P. Carpenter
Keyword(s):  
Heavy Atom ◽  
Protein Crystals ◽  
Data Sets ◽  
Low Resolution ◽  
Heavy Atoms ◽  
Density Maps ◽  
Resolution Electron ◽  
First Choice ◽  
First Time ◽  
Resolution Data

Heavy-atom derivatization is one of the oldest techniques for obtaining phase information for protein crystals and, although it is no longer the first choice, it remains a useful technique for obtaining phases for unknown structures and for low-resolution data sets. It is also valuable for confirming the chain trace in low-resolution electron-density maps. This overview provides a summary of the technique and is aimed at first-time users of the method. It includes guidelines on when to use it, which heavy atoms are most likely to work, how to prepare heavy-atom solutions, how to derivatize crystals and how to determine whether a crystal is in fact a derivative.

Use of Patterson-based methods automatically to determine the structures of heavy-atom-containing proteins with up to 6000 non-hydrogen atoms in the asymmetric unit

2006 ◽  
Vol 39 (5) ◽  
pp. 728-734 ◽  
Author(s):  
Maria Cristina Burla ◽  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Liberato De Caro ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Protein Data Bank ◽  
Heavy Atom ◽  
Data Bank ◽  
Atomic Resolution ◽  
Asymmetric Unit ◽  
Hydrogen Atoms ◽  
Heavy Atoms ◽  
Density Maps ◽  
Resolution Data

The Patterson superposition methods described by Burlaet al.[J. Appl. Cryst.(2006),39, 527–535], based on the use of the `multiple implication functions', have been enriched by supplementary filtering techniques based on some general (resolution-dependent) features of both the Patterson and the electron density maps. The method has been implemented in a modified version of the programSIR2004and tested using a set of 20 crystal structures selected from the Protein Data Bank, having a number of non-hydrogen atoms in the asymmetric unit larger than 2000, atomic resolution data and some heavy atoms (equal to or heavier than Ca). The new phasing procedure is able to solve most of the test structures, among which there are two proteins with more than 6000 non-hydrogen atoms in the asymmetric unit, so extending by far the complexity today commonly considered as the limit for Patterson-based methods (i.e.about 2000 non-hydrogen atoms).

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