scholarly journals New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences

2017 ◽  
Vol 37 (4) ◽  
Author(s):  
John R. Helliwell
Keyword(s):  
Crystal Structure ◽  
Data Bank ◽  
Crystal Structure Analysis ◽  
Public Understanding ◽  
Biological Macromolecules ◽  
Hydrogen Atoms ◽  
X Ray ◽  
The Public ◽  
X Ray Crystallography ◽  
Chemical Catalysis

Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 ‘small molecule’ crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography’s role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.

Studies Directed Towards the Total Synthesis of Anticapsin. X-Ray Crystal-Structure of (1RS,2SR,4RS,5RS,6SR)-5-Hydroxy-2-phthalimido-1-trimethylsilyloxy-bicyclo[2.2.2]octane-2,6-carbolactone

1990 ◽  
Vol 43 (11) ◽  
pp. 1827 ◽  
Author(s):  
MJ Crossley ◽  
TW Hambley ◽  
AW Stamford
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Total Synthesis ◽  
Synthetic Approach ◽  
Hydrogen Atoms ◽  
Full Matrix ◽  
X Ray ◽  
X Ray Crystallography ◽  
Relative Stereochemistry ◽  
Atomic Parameters

The relative stereochemistry of methyl 2-phthalimido-1- trimethylsilyloxybicyclo[2.2.2]oct-5-ene-2-carboxylate (9) and its 5,6-epoxide (10), intermediates in a synthetic approach to the amino acid antibiotic anticapsin, were established by the TiCl4-mediated cyclization of (10) to the carbolactone (12); the structure of which was proved by single-crystal X-ray crystallography. Full-matrix least- squares refinement of all atomic parameters with individual isotropic thermal parameters for the hydrogen atoms by using 1446 reflections converged at R 0.036. Crystals of (12) are monoclinic, P21/c, a 12.342(3), b 12.239(2), c 13.405(3) Ǻ, β 99.34(2)°, Z 4.

Electron Donor-Acceptor Compounds. Synthesis and Structure of 5-(1,4-Benzoquinone-2-yl)-10,15,20-trialkylporphyrins

1998 ◽  
Vol 53 (9) ◽  
pp. 1021-1030 ◽  
Author(s):  
Steffen Runge ◽  
Mathias O. Senge
Keyword(s):  
Crystal Structure ◽  
Structure Analysis ◽  
Supramolecular Structure ◽  
Crystal Structure Analysis ◽  
Free Base ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Polymeric Chains ◽  
Donor Acceptor

Abstract A series of 5-(benzoquinone)-10,15,20-trialkylporphyrins was synthesized via cross condensation of the respective aldehydes, 2,5-dimethoxybenzaldehyde and pyrrole followed by demethylation with BBr3 and oxidation with PbO2. This method worked reasonably well for compounds bearing the benzoquinone substituent and butyl, isopropyl, 1 -methylpropyl and 2-ethylpropyl residues (2a-d). The free base porphyrin quinones were converted into the zinc(II) complexes (3a-d) all of which showed remarkable stability for porphyrin quinones. The zinc(II) complex 3c bearing isopropyl residues was investigated by X-ray crystallography and showed a supramolecular structure consisting of polymeric chains facilitated by coordina­tion of a benzoquinone oxygen to a neighboring zinc(II) center. Attempts to synthesize a 5-(benzoquinone)-10,15,20-tris(terr-butylporphyrin) resulted in the formation of a yellow porphomethene (4), which could not be oxidized further. A crystal structure analysis of 4, the first for a free base porphomethene, shows an extremely twisted conformation with syn-orientation of the three tert-butyl groups. The results indicate that new methods will have to be developed for the synthesis of nonplanar porphyrin quinones.

Crystal structure analysis of molecular dynamics using synchrotron X-rays

CrystEngComm ◽  
2015 ◽  
Vol 17 (46) ◽  
pp. 8786-8795 ◽  
Author(s):  
Manabu Hoshino ◽  
Shin-ichi Adachi ◽  
Shin-ya Koshihara
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
X Rays ◽  
X Ray ◽  
X Ray Crystallography

X-ray crystallography using synchrotron X-rays enables observation of molecular dynamics in a crystal.

scholarly journals Why crystal structure analysis works: a one-dimensional crystallography teaching tool

2015 ◽  
Vol 48 (3) ◽  
pp. 901-905 ◽  
Author(s):  
A. Alan Pinkerton
Keyword(s):  
Crystal Structure ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
Teaching Tool ◽  
One Dimensional ◽  
X Ray ◽  
X Ray Crystallography ◽  
Scientific Calculator ◽  
Hypothetical Structure

A teaching tool is proposed to help beginner students of crystallography understand how crystallographic calculations work. Examples of the most important methods taught in X-ray crystallography courses have been adapted to a one-dimensional hypothetical structure. All calculations can be carried out in class with a scientific calculator or by using a simple spreadsheet.

scholarly journals X-ray crystal structure analysis of 5-bromospiro[indoline-3,7'-pyrano[3,2-C:5,6-C']dichromene]-2,6',8'-trione

2021 ◽  
Vol 12 (2) ◽  
pp. 187-191
Author(s):  
Varun Sharma ◽  
Bubun Banerjee ◽  
Gurpreet Kaur ◽  
Vivek Kumar Gupta
Keyword(s):  
Crystal Structure ◽  
Direct Methods ◽  
Crystal Structure Analysis ◽  
One Pot ◽  
X Ray ◽  
X Ray Crystallography ◽  
Naturally Occurring ◽  
Three Component Reaction ◽  
Ft Ir ◽  
Solvent Molecules

An analog of spirooxindole[pyrano-bis-2H-l-benzopyran] derivatives namely 5-bromospiro [indoline-3,7'-pyrano[3,2-c:5,6-c']dichromene]-2,6',8'-trione was synthesized via one-pot pseudo three-component reaction of one equivalent of 5-bromoisatin and two equivalents of 4-hydroxycoumarin using mandelic acid as a naturally occurring organo catalyst in aqueous ethanol under reflux conditions. The synthesized compound was characterized by FT-IR, 1H NMR, 13C NMR, and HRMS data. Crystal structure was determined by using single X-ray crystallography technique. It was found that the crystals are triclinic with space group P-1, C108H60Br4N4O29S2: a = 11.8333(6) Å, b = 12.8151(6) Å, c = 17.1798(8) Å, α = 77.317(4)°, β = 74.147(4)°, γ = 66.493(5)°, V = 2280.0(2) Å3, Z = 1, T = 149.99(10) K, μ(MoKα) = 1.902 mm-1, Dcalc = 1.647 g/cm3, 11545 reflections measured (3.836° ≤ 2Θ ≤ 50.998°), 8310 unique (Rint = 0.0488, Rsigma = 0.0875) which were used in all calculations. The final R1 was 0.0622 (I > 2σ(I)) and wR2 was 0.1994 (all data). The crystal structure was solved by direct methods and refined by full-matrix least-squares procedure to a final R-value of 0.0622 for 6264 observed reflections. The crystal structure was stabilized by an elaborate system of N-H···O, O-H···O, C-H···π, and π···π interactions involving solvent molecules to form supramolecular structure.

scholarly journals The refinement of atomic parameters by the technique known in X-ray crystallography as ‘the method of steepest descents’

1949 ◽  
Vol 197 (1050) ◽  
pp. 336-355 ◽  
Keyword(s):  
Crystal Structure ◽  
Structure Analysis ◽  
Relaxation Method ◽  
Crystal Structure Analysis ◽  
Actual Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Complete Discussion ◽  
General Configuration ◽  
Atomic Parameters

This paper is the first of a proposed set of three in which applications of the methods of ‘steepest descents’ are made to the problems of crystal structure analysis. The proposed programme is in three parts: (1) Working details of the method. (2) A discussion of the accuracy and convergence of the method. (3) Examples of the use of the method in actual structure determination. The present paper forms the first of this set and is complete in itself. A discussion of the normal methods of structure analysis results in a formulation of the problem as one of minimization, and leads naturally to the idea of optimum procedures for this purpose. Three techniques are derived from a unified presentation: ( a ) the ‘relaxation’ method, ( b ) the ‘least squares’ refinement, ( c ) the method of ‘steepest descents’. These are examined in detail and their virtues and defects noted. A complete discussion of the application of the steepest descent procedure to various types of structure analysis is given and techniques are derived for the cases of: refinement of a set of parameters already reasonably good; refinement of a structure where general configuration but not orientation is known; and refinement of structures given by electron densities on a lattice. Several variants of the process are given, in one of which only those planes of zero observed intensity being used; this gives a process which is independent of phase angle values and should be useful in the case of structures for which no chemical data is available.

Reflections on the Many Facets of Protein Microcrystallography

2014 ◽  
Vol 67 (12) ◽  
pp. 1793 ◽  
Author(s):  
Marion Boudes ◽  
Damià Garriga ◽  
Fasséli Coulibaly
Keyword(s):  
Structural Biology ◽  
State Of The Art ◽  
Data Bank ◽  
Biological Macromolecules ◽  
Structure Based Drug Design ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Many ◽  
The Impact

The use of X-ray crystallography for the structure determination of biological macromolecules has experienced a steady expansion over the last 20 years with the Protein Data Bank growing from <1000 deposited structures in 1992 to >100 000 in 2014. The large number of structures determined each year not only reflects the impact of X-ray crystallography on many disciplines in the biological and medical fields but also its accessibility to non-expert laboratories. Thus protein crystallography is now largely a mainstream research technique and is routinely integrated in high-throughput pipelines such as structural genomics projects and structure-based drug design. Yet, significant frontiers remain that continuously require methodological developments. In particular, membrane proteins, large assemblies, and proteins from scarce natural sources still represent challenging targets for which obtaining the large diffracting crystals required for classical crystallography is often difficult. These limitations have fostered the emergence of microcrystallography, novel approaches in structural biology that collectively aim at determining structures from the smallest crystals. Here, we review the state of the art of macromolecular microcrystallography and recent progress achieved in this field.

scholarly journals Validation of ligands in macromolecular structures determined by X-ray crystallography

2018 ◽  
Vol 74 (3) ◽  
pp. 228-236 ◽  
Author(s):  
Oliver S. Smart ◽  
Vladimír Horský ◽  
Swanand Gore ◽  
Radka Svobodová Vařeková ◽  
Veronika Bendová ◽  
...  
Keyword(s):  
Physical Chemistry ◽  
Electron Density ◽  
Data Bank ◽  
Atomic Level ◽  
Biological Macromolecules ◽  
X Ray ◽  
Validation Metrics ◽  
X Ray Crystallography ◽  
Small Molecule Ligands

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) play a crucial role in structure-guided drug discovery and design, and also provide atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. The quality with which small-molecule ligands have been modelled in Protein Data Bank (PDB) entries has been, and continues to be, a matter of concern for many investigators. Correctly interpreting whether electron density found in a binding site is compatible with the soaked or co-crystallized ligand or represents water or buffer molecules is often far from trivial. The Worldwide PDB validation report (VR) provides a mechanism to highlight any major issues concerning the quality of the data and the model at the time of deposition and annotation, so the depositors can fix issues, resulting in improved data quality. The ligand-validation methods used in the generation of the current VRs are described in detail, including an examination of the metrics to assess both geometry and electron-density fit. It is found that the LLDF score currently used to identify ligand electron-density fit outliers can give misleading results and that better ligand-validation metrics are required.

A comparison of X-ray small-angle scattering results to crystal structure analysis and other physical techniques in the field of biological macromolecules

1978 ◽  
Vol 11 (1) ◽  
pp. 39-70 ◽  
Author(s):  
O. Kratky ◽  
I. Pilz
Keyword(s):  
Crystal Structure ◽  
Structure Analysis ◽  
Small Angle ◽  
Quaternary Structure ◽  
Heavy Atom ◽  
Crystal Structure Analysis ◽  
Small Angle Scattering ◽  
Biological Macromolecules ◽  
X Ray ◽  
Angle Scattering

In principle, there exist two ways to contribute to structure determination of macromolecules by X-ray diffraction: (a) by analysing diffraction data obtained from the crystalline state, and (b) by interpretation of X-ray small-angle scattering from particles in solution.The brilliant achievements of X-ray crystal-structure analysis of macromolecules, initiated by the works of Perutz on heamoglobin and Kendrew on myoglobin, are well known and it is evident that its detailed elution of secondary, tertiary and quaternary structure cannot be matched by any other means. However, a number of necessary prerequisites for a successful application, as, for example, the availability of well-defined crystals and heavy atom labelled derivatives thereof to surmount the problem of phase determination are not always given.

scholarly journals Durward W. J. Cruickshank. 7 March 1924—13 July 2007

2018 ◽  
Vol 65 ◽  
pp. 71-87
Author(s):  
B. Beagley ◽  
J. R. Helliwell
Keyword(s):  
Crystal Structure ◽  
Structure Analysis ◽  
Materials Science ◽  
Measurement Techniques ◽  
Three Dimensional ◽  
Data Bank ◽  
Crystal Structure Analysis ◽  
Molecular Structures ◽  
Three Dimensions ◽  
X Ray

Durward Cruickshank was an eminent crystallographer and structural chemist, whose mathematical abilities transformed the precision of the molecular structures determined in three dimensions by X-ray crystal structure analysis. This technique is very widely applied to determine the three-dimensional (3D) shapes of molecules of importance in biology, chemistry, mineralogy, materials science and physics. Durward's first publication was on this topic, with Sir Gordon Cox. It represents a lifelong interest of Durward in the precision of crystal structure analysis and extended also to gas-phase electron diffraction. His research publications spanned an amazing 60 years and he had a direct influence on over 900 000 chemical crystal structures, the number currently determined and held in the Cambridge Structure Database alone. Proteins took his attention for research in his last decade, and his diffraction precision index (DPI) indicator of the precision of a protein structure is added regularly to entries in the Protein Data Bank. In his ‘retirement’ he contributed, with one of the authors of this memoir, J.R.H., and various colleagues in the UK and the USA, to the development of the ‘Laue diffraction’ white beam synchrotron method, applied today to sub-nanosecond X-ray crystallography measurement techniques, and also to study micron sized, i.e. tiny, crystal samples. The method has also led ultimately to more effective exploitation of neutron beams from research reactors for crystallographic studies of the hydrogenation details of molecules.

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