X-ray crystallography
X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the positions of the atoms in the crystal can be determined, as well as their chemical bonds, crystallographic disorder, and various other information.
Since many materials form crystals—such as
X-ray crystallography is related to multiple other methods for determining atomic structures. Similar diffraction patterns can be produced by scattering electrons or
History
Crystals, though long admired for their regularity and symmetry, were not investigated scientifically until the 17th century.
The idea that crystals could be used as a
After Von Laue's pioneering research, the field developed rapidly, most notably by physicists
The earliest structures were simple inorganic crystals and minerals, but even these revealed fundamental laws of physics and chemistry. The first atomic-resolution structure to be "solved" (i.e., determined) in 1914 was that of
The structure of
Contributions in different areas
Chemistry
X-ray crystallography has led to a better understanding of
The first structure of an organic compound,
In the 1920s,
The distance between two bonded atoms is a sensitive measure of the bond strength and its
Materials science and mineralogy
The application of X-ray crystallography to
On October 17, 2012, the
Biological macromolecular crystallography
X-ray crystallography of biological molecules took off with
Crystal structures of proteins (which are irregular and hundreds of times larger than cholesterol) began to be solved in the late 1950s, beginning with the structure of
Methods
Overview of single-crystal X-ray diffraction
The oldest and most precise method of X-ray crystallography is single-crystal X-ray diffraction, in which a beam of X-rays strikes a single crystal, producing scattered beams which are recorded as the crystal is gradually rotated.[a] For single crystals of sufficient purity and regularity, X-ray diffraction data can determine the mean chemical bond lengths and angles to within a few thousandths of an angstrom and to within a few tenths of a degree, respectively. The atoms in a crystal are not static, but oscillate about their mean positions, usually by less than a few tenths of an angstrom. X-ray crystallography can measure the size of these oscillations.
Two limiting cases of X-ray crystallography—"small-molecule" (which includes continuous inorganic solids) and "macromolecular" crystallography—are often used. Small-molecule crystallography typically involves crystals with fewer than 100 atoms in their asymmetric unit; such crystal structures are usually so well resolved that the atoms can be discerned as isolated "blobs" of electron density. In contrast, macromolecular crystallography often involves tens of thousands of atoms in the unit cell. Such crystal structures are generally less well-resolved; the atoms and chemical bonds appear as tubes of electron density, rather than as isolated atoms. In general, small molecules are also easier to crystallize than macromolecules; however, X-ray crystallography has proven possible even for viruses and proteins with hundreds of thousands of atoms, through improved crystallographic imaging and technology.[96]
Procedure
The technique of single-crystal X-ray crystallography has three basic steps. The first—and often most difficult—step is to obtain an adequate crystal of the material under study. The crystal should be sufficiently large (typically larger than 0.1 mm in all dimensions), pure in composition and regular in structure, with no significant internal
In the second step, the crystal is placed in an intense beam of X-rays, usually of a single wavelength (monochromatic X-rays), producing the regular pattern of reflections. The angles and intensities of diffracted X-rays are measured, with each compound having a unique diffraction pattern.[97] As the crystal is gradually rotated, previous reflections disappear and new ones appear; the intensity of every spot is recorded at every orientation of the crystal. Multiple data sets may have to be collected, with each set covering slightly more than half a full rotation of the crystal and typically containing tens of thousands of reflections.
In the third step, these data are combined computationally with complementary chemical information to produce and refine a model of the arrangement of atoms within the crystal. The final, refined model of the atomic arrangement—now called a crystal structure—is usually stored in a public database.
Crystallization
Although crystallography can be used to characterize the disorder in an impure or irregular crystal, crystallography generally requires a pure crystal of high regularity to solve the structure of a complicated arrangement of atoms. Pure, regular crystals can sometimes be obtained from natural or synthetic materials, such as samples of metals, minerals or other macroscopic materials. The regularity of such crystals can sometimes be improved with macromolecular crystal
Small-molecule and macromolecular crystallography differ in the range of possible techniques used to produce diffraction-quality crystals. Small molecules generally have few degrees of conformational freedom, and may be crystallized by a wide range of methods, such as chemical vapor deposition and recrystallization. By contrast, macromolecules generally have many degrees of freedom and their crystallization must be carried out so as to maintain a stable structure. For example, proteins and larger RNA molecules cannot be crystallized if their tertiary structure has been unfolded; therefore, the range of crystallization conditions is restricted to solution conditions in which such molecules remain folded.
Protein crystals are almost always grown in solution. The most common approach is to lower the solubility of its component molecules very gradually; if this is done too quickly, the molecules will precipitate from solution, forming a useless dust or amorphous gel on the bottom of the container. Crystal growth in solution is characterized by two steps: nucleation of a microscopic crystallite (possibly having only 100 molecules), followed by growth of that crystallite, ideally to a diffraction-quality crystal.[102][103] The solution conditions that favor the first step (nucleation) are not always the same conditions that favor the second step (subsequent growth). The solution conditions should disfavor the first step (nucleation) but favor the second (growth), so that only one large crystal forms per droplet. If nucleation is favored too much, a shower of small crystallites will form in the droplet, rather than one large crystal; if favored too little, no crystal will form whatsoever. Other approaches involve crystallizing proteins under oil, where aqueous protein solutions are dispensed under liquid oil, and water evaporates through the layer of oil. Different oils have different evaporation permeabilities, therefore yielding changes in concentration rates from different percipient/protein mixture.[104]
It is difficult to predict good conditions for nucleation or growth of well-ordered crystals.
Several factors are known to inhibit or mar crystallization. The growing crystals are generally held at a constant temperature and protected from shocks or vibrations that might disturb their crystallization. Impurities in the molecules or in the crystallization solutions are often inimical to crystallization. Conformational flexibility in the molecule also tends to make crystallization less likely, due to entropy. Molecules that tend to self-assemble into regular helices are often unwilling to assemble into crystals.[citation needed] Crystals can be marred by twinning, which can occur when a unit cell can pack equally favorably in multiple orientations; although recent advances in computational methods may allow solving the structure of some twinned crystals. Having failed to crystallize a target molecule, a crystallographer may try again with a slightly modified version of the molecule; even small changes in molecular properties can lead to large differences in crystallization behavior.
Data collection
Mounting the crystal
The crystal is mounted for measurements so that it may be held in the X-ray beam and rotated. There are several methods of mounting. In the past, crystals were loaded into glass capillaries with the crystallization solution (the mother liquor). Nowadays, crystals of small molecules are typically attached with oil or glue to a glass fiber or a loop, which is made of nylon or plastic and attached to a solid rod. Protein crystals are scooped up by a loop, then flash-frozen with liquid nitrogen.[108] This freezing reduces the radiation damage of the X-rays, as well as the noise in the Bragg peaks due to thermal motion (the Debye-Waller effect). However, untreated protein crystals often crack if flash-frozen; therefore, they are generally pre-soaked in a cryoprotectant solution before freezing.[109] This pre-soak may itself cause the crystal to crack, ruining it for crystallography. Generally, successful cryo-conditions are identified by trial and error.
The capillary or loop is mounted on a goniometer, which allows it to be positioned accurately within the X-ray beam and rotated. Since both the crystal and the beam are often very small, the crystal must be centered within the beam to within ~25 micrometers accuracy, which is aided by a camera focused on the crystal. The most common type of goniometer is the "kappa goniometer", which offers three angles of rotation: the ω angle, which rotates about an axis perpendicular to the beam; the κ angle, about an axis at ~50° to the ω axis; and, finally, the φ angle about the loop/capillary axis. When the κ angle is zero, the ω and φ axes are aligned. The κ rotation allows for convenient mounting of the crystal, since the arm in which the crystal is mounted may be swung out towards the crystallographer. The oscillations carried out during data collection (mentioned below) involve the ω axis only. An older type of goniometer is the four-circle goniometer, and its relatives such as the six-circle goniometer.
Recording the reflections
The relative intensities of the reflections provides information to determine the arrangement of molecules within the crystal in atomic detail. The intensities of these reflections may be recorded with photographic film, an area detector (such as a pixel detector) or with a charge-coupled device (CCD) image sensor. The peaks at small angles correspond to low-resolution data, whereas those at high angles represent high-resolution data; thus, an upper limit on the eventual resolution of the structure can be determined from the first few images. Some measures of diffraction quality can be determined at this point, such as the mosaicity of the crystal and its overall disorder, as observed in the peak widths. Some pathologies of the crystal that would render it unfit for solving the structure can also be diagnosed quickly at this point.
One set of spots is insufficient to reconstruct the whole crystal; it represents only a small slice of the full three dimensional set. To collect all the necessary information, the crystal must be rotated step-by-step through 180°, with an image recorded at every step; actually, slightly more than 180° is required to cover
Multiple data sets may be necessary for certain
Crystal symmetry, unit cell, and image scaling
The recorded series of two-dimensional diffraction patterns, each corresponding to a different crystal orientation, is converted into a three-dimensional set. Data processing begins with indexing the reflections. This means identifying the dimensions of the unit cell and which image peak corresponds to which position in reciprocal space. A byproduct of indexing is to determine the symmetry of the crystal, i.e., its space group. Some space groups can be eliminated from the beginning. For example, reflection symmetries cannot be observed in chiral molecules; thus, only 65 space groups of 230 possible are allowed for protein molecules which are almost always chiral. Indexing is generally accomplished using an autoindexing routine.[111] Having assigned symmetry, the data is then integrated. This converts the hundreds of images containing the thousands of reflections into a single file, consisting of (at the very least) records of the Miller index of each reflection, and an intensity for each reflection (at this state the file often also includes error estimates and measures of partiality (what part of a given reflection was recorded on that image)).
A full data set may consist of hundreds of separate images taken at different orientations of the crystal. These have to be merged and scaled usingpeaks appear in two or more images (merging) and scaling so there is a consistent intensity scale. Optimizing the intensity scale is critical because the relative intensity of the peaks is the key information from which the structure is determined. The repetitive technique of crystallographic data collection and the often high symmetry of crystalline materials cause the diffractometer to record many symmetry-equivalent reflections multiple times. This allows calculating the symmetry-related R-factor, a reliability index based upon how similar are the measured intensities of symmetry-equivalent reflections,[clarification needed] thus assessing the quality of the data.
Initial phasing
The intensity of each diffraction 'spot' is proportional to the modulus squared of the structure factor. The structure factor is a complex number containing information relating to both the amplitude and phase of a wave. In order to obtain an interpretable electron density map, both amplitude and phase must be known (an electron density map allows a crystallographer to build a starting model of the molecule). The phase cannot be directly recorded during a diffraction experiment: this is known as the phase problem. Initial phase estimates can be obtained in a variety of ways:
- Ab initio phasing or direct methods – This is usually the method of choice for small molecules (<1000 non-hydrogen atoms), and has been used successfully to solve the phase problems for small proteins. If the resolution of the data is better than 1.4 Å (140 pm), direct methods can be used to obtain phase information, by exploiting known phase relationships between certain groups of reflections.[112][113]
- Molecular replacement – if a related structure is known, it can be used as a search model in molecular replacement to determine the orientation and position of the molecules within the unit cell. The phases obtained this way can be used to generate electron density maps.[114]
- SAD phasing) – the X-ray wavelength may be scanned past an absorption edge[b] of an atom, which changes the scattering in a known way. By recording full sets of reflections at three different wavelengths (far below, far above and in the middle of the absorption edge) one can solve for the substructure of the anomalously diffracting atoms and hence the structure of the whole molecule. The most popular method of incorporating anomalous scattering atoms into proteins is to express the protein in a methionine auxotroph (a host incapable of synthesizing methionine) in a media rich in seleno-methionine, which contains selenium atoms. A multi-wavelength anomalous dispersion (MAD) experiment can then be conducted around the absorption edge, which should then yield the position of any methionine residues within the protein, providing initial phases.[115]
- Heavy atom methods (multiple isomorphous replacement) – If electron-dense metal atoms can be introduced into the crystal, direct methods or Patterson-space methods can be used to determine their location and to obtain initial phases. Such heavy atoms can be introduced either by soaking the crystal in a heavy atom-containing solution, or by co-crystallization (growing the crystals in the presence of a heavy atom). As in multi-wavelength anomalous dispersion phasing, the changes in the scattering amplitudes can be interpreted to yield the phases. Although this is the original method by which protein crystal structures were solved, it has largely been superseded by multi-wavelength anomalous dispersion phasing with selenomethionine.[114]
Model building and phase refinement
Having obtained initial phases, an initial model can be built. The atomic positions in the model and their respective
where F is the structure factor. A similar quality criterion is Rfree, which is calculated from a subset (~10%) of reflections that were not included in the structure refinement. Both R factors depend on the resolution of the data. As a rule of thumb, Rfree should be approximately the resolution in angstroms divided by 10; thus, a data-set with 2 Å resolution should yield a final Rfree ~ 0.2. Chemical bonding features such as stereochemistry, hydrogen bonding and distribution of bond lengths and angles are complementary measures of the model quality. In iterative model building, it is common to encounter phase bias or model bias: because phase estimations come from the model, each round of calculated map tends to show density wherever the model has density, regardless of whether there truly is a density. This problem can be mitigated by maximum-likelihood weighting and checking using omit maps.[118]
It may not be possible to observe every atom in the asymmetric unit. In many cases, crystallographic disorder smears the electron density map. Weakly scattering atoms such as hydrogen are routinely invisible. It is also possible for a single atom to appear multiple times in an electron density map, e.g., if a protein sidechain has multiple (<4) allowed conformations. In still other cases, the crystallographer may detect that the covalent structure deduced for the molecule was incorrect, or changed. For example, proteins may be cleaved or undergo post-translational modifications that were not detected prior to the crystallization.
Disorder
A common challenge in refinement of crystal structures results from crystallographic disorder. Disorder can take many forms but in general involves the coexistence of two or more species or conformations. Failure to recognize disorder results in flawed interpretation. Pitfalls from improper modeling of disorder are illustrated by the discounted hypothesis of bond stretch isomerism.[119] Disorder is modelled with respect to the relative population of the components, often only two, and their identity. In structures of large molecules and ions, solvent and counterions are often disordered.
Applied computational data analysis
The use of computational methods for the powder X-ray diffraction data analysis is now generalized. It typically compares the experimental data to the simulated diffractogram of a model structure, taking into account the instrumental parameters, and refines the structural or microstructural parameters of the model using least squares based minimization algorithm. Most available tools allowing phase identification and structural refinement are based on the Rietveld method,[120][121] some of them being open and free software such as FullProf Suite,[122][123] Jana2006,[124] MAUD,[125][126][127] Rietan,[128] GSAS,[129] etc. while others are available under commercial licenses such as Diffrac.Suite TOPAS,[130] Match!,[131] etc. Most of these tools also allow Le Bail refinement (also referred to as profile matching), that is, refinement of the cell parameters based on the Bragg peaks positions and peak profiles, without taking into account the crystallographic structure by itself. More recent tools allow the refinement of both structural and microstructural data, such as the FAULTS program included in the FullProf Suite,[132] which allows the refinement of structures with planar defects (e.g. stacking faults, twinnings, intergrowths).
Deposition of the structure
Once the model of a molecule's structure has been finalized, it is often deposited in a
X-ray sources
Rotating anode
Small scale crystallography can be done with a local
X-rays are generally filtered (by use of X-ray filters) to a single wavelength (made monochromatic) and collimated to a single direction before they are allowed to strike the crystal. The filtering not only simplifies the data analysis, but also removes radiation that degrades the crystal without contributing useful information. Collimation is done either with a collimator (basically, a long tube) or with a clever arrangement of gently curved mirrors. Mirror systems are preferred for small crystals (under 0.3 mm) or with large unit cells (over 150 Å).
Microfocus tube
A more recent development is the microfocus tube, which can deliver at least as high a beam flux (after collimation) as rotating-anode sources but only require a beam power of a few tens or hundreds of watts rather than requiring several kilowatts.
Synchrotron radiation
Synchrotron radiation sources are some of the brightest light sources on earth and are some of the most powerful tools available to X-ray crystallographers. X-ray beams are generated in large machines called synchrotrons which accelerate electrically charged particles, often electrons, to nearly the speed of light and confine them in a (roughly) circular loop using magnetic fields.
Synchrotrons are generally national facilities, each with several dedicated
Using synchrotron radiation frequently has specific requirements for X-ray crystallography. The intense
Free-electron laser
Free-electron lasers have been developed for use in X-ray crystallography.[135] These are the brightest X-ray sources currently available; with the X-rays coming in femtosecond bursts. The intensity of the source is such that atomic resolution diffraction patterns can be resolved for crystals otherwise too small for collection. However, the intense light source also destroys the sample,[136] requiring multiple crystals to be shot. As each crystal is randomly oriented in the beam, hundreds of thousands of individual diffraction images must be collected in order to get a complete data set. This method, serial femtosecond crystallography, has been used in solving the structure of a number of protein crystal structures, sometimes noting differences with equivalent structures collected from synchrotron sources.[137]
Introduction to x-ray diffraction theory
Basics
Crystals are regular arrays of atoms, and X-rays are electromagnetic waves. Atoms scatter X-ray waves, primarily through the atoms' electrons. Just as an ocean wave striking a lighthouse produces secondary circular waves emanating from the lighthouse, so an X-ray striking an electron produces secondary spherical waves emanating from the electron. This phenomenon is known as
An intuitive understanding of X-ray diffraction can be obtained from the
A reflection is said to be indexed when its Miller indices (or, more correctly, its
Ewald's sphere
Each X-ray diffraction pattern represents a spherical slice of reciprocal space, as may be seen by the Ewald sphere construction. For a given incident wavevector k0 the only wavevectors with the same energy lie on the surface of a sphere. In the diagram, the wavevector k1 lies on the Ewald sphere and also is at a reciprocal lattice vector g1 so satisfies Bragg's law. In contrast the wavevector k2 differs from the reciprocal lattice point and g2 by the vector s which is called the excitation error. For large single crystals primarily used in crystallography only the Bragg's law case matters; for electron diffraction and some other types of x-ray diffraction non-zero values of the excitation error also matter.
Scattering amplitudes
X-ray scattering is determined by the density of electrons within the crystal. Since the energy of an X-ray is much greater than that of a valence electron, the scattering may be modeled as Thomson scattering, the elastic interaction of an electromagnetic ray with a charged particle.
The intensity of Thomson scattering for one particle with mass m and elementary charge q is:[138]
Hence the atomic nuclei, which are much heavier than an electron, contribute negligibly to the scattered X-rays. Consequently, the coherent scattering detected from an atom can be accurately approximated by analyzing the collective scattering from the electrons in the system.[139]
The incoming X-ray beam has a polarization and should be represented as a vector wave; however, for simplicity, let it be represented here as a scalar wave. We also ignore the complication of the time dependence of the wave and just concentrate on the wave's spatial dependence. Plane waves can be represented by a wave vector kin, and so the incoming wave at time t = 0 is given by
At position r within the sample, let there be a density of scatterers f(r); these scatterers produce a scattered spherical wave of amplitude proportional to the local amplitude of the incoming wave times the number of scatterers in a small volume dV about r
where S is the proportionality constant.
Consider the fraction of scattered waves that leave with an outgoing wave-vector of kout and strike a screen (detector) at rscreen. Since no energy is lost (elastic, not inelastic scattering), the wavelengths are the same as are the magnitudes of the wave-vectors |kin| = |kout|. From the time that the photon is scattered at r until it is absorbed at rscreen, the photon undergoes a change in phase
The net radiation arriving at rscreen is the sum of all the scattered waves throughout the crystal
which may be written as a Fourier transform
where g = kout – kin is a reciprocal lattice vector that satisfies Bragg's law and the Ewald construction mentioned above. The measured intensity of the reflection will be square of this amplitude
Related scattering techniques
Other X-ray techniques
Other forms of elastic X-ray scattering besides single-crystal diffraction include
These scattering methods generally use monochromatic X-rays, which are restricted to a single wavelength with minor deviations. A broad spectrum of X-rays (that is, a blend of X-rays with different wavelengths) can also be used to carry out X-ray diffraction, a technique known as the Laue method. This is the method used in the original discovery of X-ray diffraction. Laue scattering provides much structural information with only a short exposure to the X-ray beam, and is therefore used in structural studies of very rapid events (time resolved crystallography). However, it is not as well-suited as monochromatic scattering for determining the full atomic structure of a crystal and therefore works better with crystals with relatively simple atomic arrangements.
The Laue back reflection mode records X-rays scattered backwards from a broad spectrum source. This is useful if the sample is too thick for X-rays to transmit through it. The diffracting planes in the crystal are determined by knowing that the normal to the diffracting plane bisects the angle between the incident beam and the diffracted beam. A Greninger chart can be used[140] to interpret the back reflection Laue photograph.
Electron diffraction
Because they interact via the Coulomb forces the scattering of electrons by matter is 1000 or more times stronger than for X-rays. Hence electron beams produce strong multiple or dynamical scattering even for relatively thin crystals (>10 nm). While there are similarities between the diffraction of X-rays and electrons, as can be found in the book by John M. Cowley,[141] the approach is different as it is based upon the original approach of Hans Bethe[142] and solving Schrödinger equation for relativistic electrons, rather than a kinematical or Bragg's law approach. Information about very small regions, down to single atoms is possible. The range of applications for electron diffraction, transmission electron microscopy and transmission electron crystallography with high energy electrons is extensive; see the relevant links for more information and citations. In addition to transmission methods, low-energy electron diffraction[143] is a technique where electrons are back-scattered off surfaces and has been extensively used to determine surface structures at the atomic scale, and reflection high-energy electron diffraction is another which is extensively used to monitor thin film growth.[144]
Neutron diffraction
Neutron diffraction is used for structure determination, although it has been difficult to obtain intense, monochromatic beams of neutrons in sufficient quantities. Traditionally, nuclear reactors have been used, although sources producing neutrons by spallation are becoming increasingly available. Being uncharged, neutrons scatter more from the atomic nuclei rather than from the electrons. Therefore, neutron scattering is useful for observing the positions of light atoms with few electrons, especially hydrogen, which is essentially invisible in X-ray diffraction. Neutron scattering also has the property that the solvent can be made invisible by adjusting the ratio of normal water, H2O, and heavy water, D2O.
Contribution of women to X-ray crystallography
A number of women were pioneers in X-ray crystallography at a time when they were excluded from most other branches of physical science.[145]
Kathleen Lonsdale was a research student of William Henry Bragg, who had 11 women research students out of a total of 18. She is known for both her experimental and theoretical work. Lonsdale joined his crystallography research team at the Royal Institution in London in 1923, and after getting married and having children, went back to work with Bragg as a researcher. She confirmed the structure of the benzene ring, carried out studies of diamond, was one of the first two women to be elected to the Royal Society in 1945, and in 1949 was appointed the first female tenured professor of chemistry and head of the Department of crystallography at University College London.[146] Lonsdale always advocated greater participation of women in science and said in 1970: "Any country that wants to make full use of all its potential scientists and technologists could do so, but it must not expect to get the women quite so simply as it gets the men. ... It is utopian, then, to suggest that any country that really wants married women to return to a scientific career, when her children no longer need her physical presence, should make special arrangements to encourage her to do so?".[147] During this period, Lonsdale began a collaboration with William T. Astbury on a set of 230 space group tables which was published in 1924 and became an essential tool for crystallographers.
In 1932 Dorothy Hodgkin joined the laboratory of the physicist John Desmond Bernal, who was a former student of Bragg, in Cambridge, UK. She and Bernal took the first X-ray photographs of crystalline proteins. Hodgkin also played a role in the foundation of the International Union of Crystallography. She was awarded the Nobel Prize in Chemistry in 1964 for her work using X-ray techniques to study the structures of penicillin, insulin and vitamin B12. Her work on penicillin began in 1942 during the war and on vitamin B12 in 1948. While her group slowly grew, their predominant focus was on the X-ray analysis of natural products. She is the only British woman ever to have won a Nobel Prize in a science subject.
Rosalind Franklin took the X-ray photograph of a DNA fibre that proved key to James Watson and Francis Crick's discovery of the double helix, for which they both won the Nobel Prize for Physiology or Medicine in 1962. Watson revealed in his autobiographic account of the discovery of the structure of DNA, The Double Helix,[148] that he had used Franklin's X-ray photograph without her permission. Franklin died of cancer in her 30s, before Watson received the Nobel Prize. Franklin also carried out important structural studies of carbon in coal and graphite, and of plant and animal viruses.
Isabella Karle of the United States Naval Research Laboratory developed an experimental approach to the mathematical theory of crystallography. Her work improved the speed and accuracy of chemical and biomedical analysis. Yet only her husband Jerome shared the 1985 Nobel Prize in Chemistry with Herbert Hauptman, "for outstanding achievements in the development of direct methods for the determination of crystal structures". Other prize-giving bodies have showered Isabella with awards in her own right.
Women have written many textbooks and research papers in the field of X-ray crystallography. For many years Lonsdale edited the International Tables for Crystallography, which provide information on crystal lattices, symmetry, and space groups, as well as mathematical, physical and chemical data on structures.
Nobel Prizes involving X-ray crystallography
Year | Laureate | Prize | Rationale |
---|---|---|---|
1914 | Max von Laue | Physics | "For his discovery of the diffraction of X-rays by crystals"[150] |
1915 | William Henry Bragg | Physics | "For their services in the analysis of crystal structure by means of X-rays"[151] |
William Lawrence Bragg
| |||
1962 | Max F. Perutz |
Chemistry | "for their studies of the structures of globular proteins"[152] |
John C. Kendrew
| |||
1962 | James Dewey Watson |
Medicine | "For their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material"[153] |
Francis Harry Compton Crick | |||
Maurice Hugh Frederick Wilkins | |||
1964 | Dorothy Hodgkin | Chemistry | "For her determinations by X-ray techniques of the structures of important biochemical substances"[154] |
1972 | Stanford Moore | Chemistry | "For their contribution to the understanding of the connection between chemical structure and catalytic activity of the active centre of the ribonuclease molecule"[155] |
William H. Stein | |||
1976 | William N. Lipscomb | Chemistry | "For his studies on the structure of boranes illuminating problems of chemical bonding"[156] |
1985 | Jerome Karle | Chemistry | "For their outstanding achievements in developing direct methods for the determination of crystal structures"[157]
|
Herbert A. Hauptman | |||
1988 | Johann Deisenhofer | Chemistry | "For their determination of the three-dimensional structure of a photosynthetic reaction centre"[158]
|
Hartmut Michel | Chemistry | ||
Robert Huber | Chemistry | ||
1997 | John E. Walker | Chemistry | "For their elucidation of the enzymatic mechanism underlying the synthesis of adenosine triphosphate (ATP)"[159] |
2003 | Roderick MacKinnon | Chemistry | "For discoveries concerning channels in cell membranes [...] for structural and mechanistic studies of ion channels"[160] |
Peter Agre | "For discoveries concerning channels in cell membranes [...] for the discovery of water channels"[160] | ||
2006 | Roger D. Kornberg | Chemistry | "For his studies of the molecular basis of eukaryotic transcription"[161]
|
2009 | Ada E. Yonath |
Chemistry | "For studies of the structure and function of the ribosome"[162] |
Thomas A. Steitz | |||
Venkatraman Ramakrishnan
| |||
2012 | Brian Kobilka | Chemistry | "For studies of G-protein-coupled receptors"[163] |
See also
- Beevers–Lipson strip
- Bragg diffraction
- Crystallographic database
- Crystallographic point groups
- Difference density map
- Electron diffraction
- Energy-dispersive X-ray diffraction
- Flack parameter
- Grazing incidence diffraction
- Henderson limit
- International Year of Crystallography
- Multipole density formalism
- Neutron diffraction
- Powder diffraction
- Ptychography
- Scherrer equation
- Small angle X-ray scattering (SAXS)
- Structure determination
- Ultrafast x-ray
- Wide angle X-ray scattering(WAXS)
Notes
- ^ An analogous diffraction pattern may be observed by shining a laser pointer on a compact disc or DVD; the periodic spacing of the CD tracks corresponds to the periodic arrangement of atoms in a crystal.
- ^ The absorption edge is originally known from X-ray absorption spectroscopy. See "X-ray Anomalous Scattering". skuld.bmsc.washington.edu. for a guide to anomalous scattering.
References
- ISBN 3-321-00021-0.
- ^ Steno N (1669). De solido intra solidum naturaliter contento dissertationis prodromus. Florentiae.
- ^ Hessel JF (1831). Kristallometrie oder Kristallonomie und Kristallographie. Leipzig.
- ^ Bravais A (1850). "Mémoire sur les systèmes formés par des points distribués regulièrement sur un plan ou dans l'espace". Journal de l'École Polytechnique. 19: 1.
- ISBN 90-277-9029-9.
- Schönflies A(1891). Kristallsysteme und Kristallstruktur. Leipzig.
- S2CID 4016086.
- ^ . Retrieved 25 March 2022.
- ^ Barkla, Charles G. (1911). "XXXIX.The spectra of the fluorescent Röntgen radiations". Philosophical Magazine. Series 6. 22 (129): 396–412. doi:10.1080/14786440908637137.
- ^ a b Michael Eckert, Disputed discovery: the beginnings of X-ray diffraction in crystals in 1912 and its repercussions, January 2011, Acta crystallographica. Section A, Foundations of crystallography 68(1):30–39 This Laue centennial article has also been published in Zeitschrift für Kristallographie [Eckert (2012). Z. Kristallogr. 227, 27–35].
- ^ Nisio, Sigeko. "The Formation of the Sommerfeld Quantum Theory of 1916." (1974) JSHS, No.12. pp39-78.
- .
- ^ Compare: Einstein A (1909). "Über die Entwicklung unserer Anschauungen über das Wesen und die Konstitution der Strahlung" [The Development of Our Views on the Composition and Essence of Radiation]. Physikalische Zeitschrift (in German). 10: 817.. An English translation is available from Wikisource.
- ISBN 0-19-853907-X.
- .
- ^ Bragg WH (1907). "The nature of Röntgen rays". Transactions of the Royal Society of Science of Australia. 31: 94.
- S2CID 4024851.
- .
- .
- ^ a b Friedrich W, Knipping P, von Laue M (1912). "Interferenz-Erscheinungen bei Röntgenstrahlen" (PDF). Sitzungsberichte der Mathematisch-Physikalischen Classe der Königlich-Bayerischen Akademie der Wissenschaften zu München [Interference phenomena in X-rays]. 1912: 303.
- ^ Friedrich W, Knipping P, von Laue M (1912). "Interferenz-Erscheinungen bei Röntgenstrahlen" (PDF). Sitzungsberichte der Mathematisch-Physikalischen Classe der Königlich-Bayerischen Akademie der Wissenschaften zu München [Interference phenomena in X-rays]. 1912: 303.
- ^ von Laue M (1914). "Concerning the detection of x-ray interferences" (PDF). Nobel Lectures, Physics. 1901–1921. Retrieved 2009-02-18.
- ^ Dana ES, Ford WE (1932). A Textbook of Mineralogy (fourth ed.). New York: John Wiley & Sons. p. 28.
- S2CID 3952319.
- ^ Bragg WL (1913). "The Diffraction of Short Electromagnetic Waves by a Crystal". Proceedings of the Cambridge Philosophical Society. 17: 43.
- ^ Bragg WL (1914). "Die Reflexion der Röntgenstrahlen". Jahrbuch der Radioaktivität und Elektronik. 11: 350.
- JSTOR 93488.
- .
- .
- .
- ^ S2CID 3987932.
- .
- .
- ^ .
- .
- ^ Nishikawa S (1915). "Structure of some crystals of spinel group". Proc. Tokyo Math. Phys. Soc. 8: 199.
- .
- .
- ^ Aminoff G (1921). "Über die Struktur des Magnesiumhydroxids". Z. Kristallogr. 56: 505.
- .
- ^ Debije P, Scherrer P (1916). "Interferenz an regellos orientierten Teilchen im Röntgenlicht I". Physikalische Zeitschrift. 17: 277.
- ^ Friedrich W (1913). "Eine neue Interferenzerscheinung bei Röntgenstrahlen". Physikalische Zeitschrift. 14: 317.
- .
- JSTOR 94336.
- S2CID 121157442.
- .
- PMID 16576242.
- .
- ^ S2CID 4098112.
- S2CID 4105837.
- ISBN 0-8014-0333-2.
- .
- .
- .
- .
- doi:10.1038/115266a0.
- Comptes rendus hebdomadaires des séances de l'Académie des sciences. 180: 1485.
- .
- .
- .
- .
- .
- .
- .
- .
- ^ Robinson WT, Fergusson JE, Penfold BR (1963). "Configuration of Anion in CsReCl4". Proceedings of the Chemical Society of London: 116.
- S2CID 29700317.
- .
- .
- .
- S2CID 27195273.
- .
- .
- .
- .
- .
- .
- ^ a b Brown D (October 30, 2012). "NASA Rover's First Soil Studies Help Fingerprint Martian Minerals". NASA. Retrieved October 31, 2012.
- .
- .
- ^ Hume-Rothery W (1926). "Researches on the Nature, Properties and Conditions of Formation of Intermetallic Compounds (with special Reference to certain Compounds of Tin)". Journal of the Institute of Metals. 35: 295.
- doi:10.1038/120678a0.
- .
- .
- .
- .
- S2CID 4121225.
- S2CID 4162786.
- ^ "The Nobel Prize in Chemistry 1962". www.nobelprize.org. Retrieved 2018-01-31.
- ^ "Table of entries in the PDB, arranged by experimental method". Archived from the original on 2017-07-11. Retrieved 2017-07-24.
- ^ "PDB Statistics". RCSB Protein Data Bank. Retrieved 2010-02-09.
- PMID 16796557.
- S2CID 13432321.
- PMID 15320710.
- PMID 17372353.
- PMID 24476871.
- ^ "Morphology XRD Analysis | IMR TEST LABS". www.imrtest.com. Retrieved 2018-04-30.
- PMID 9761858.
- PMID 10393299.
- PMID 14674276.
- PMID 17001090.
- PMID 12718915.
- ^ Bergfors T (2016). "Protein crystallization Tutorial".
- PMID 9351804.
- PMID 15325656.
- PMID 15652248.
- PMID 15652247.
- PMID 17172760.
- PMID 15930642.
- PMID 16938450.
- PMID 10531518.
- PMID 9345626.
- PMID 10508770.
- ^ PMID 14573942.
- PMID 11006535.
- ^ From PDB file 2NRL, residues 17–32.
- ^ "Garman lab: Interconversion of lysosomal enzyme specificities – Proteopedia, life in 3D". proteopedia.org. Retrieved 2018-11-28.
- PMID 25554228.
- .
- .
- OCLC 26299196.
- ^ "IUCr". www.iucr.org. Retrieved 2019-04-06.
- ^ "Fullprof". www.ill.eu. Retrieved 2019-04-06.
- S2CID 101692863.
- ISSN 0168-583X.
- ISBN 9783486992540
- ISSN 0021-8979.
- ^ "Distribution Files for the RIETAN-FP-VENUS Package". fujioizumi.verse.jp. Retrieved 2019-04-06.
- ISSN 0021-8898.
- ^ "DIFFRAC.SUITE TOPAS - XRD Software, X-ray diffraction". Bruker.com. Retrieved 2019-04-06.
- ^ "Match! – Phase Identification from Powder Diffraction". www.crystalimpact.com. Retrieved 2019-04-06.
- ISSN 1600-5767.
- .
- PMID 26057787.
- PMID 22922042.
- S2CID 4300920.
- PMID 24357322.
- ^ Guinier A (1952). X-ray Crystallographic Technology. London: Hilger and Watts LTD. p. 271.
- OCLC 46437243.
- S2CID 101434745.
- OCLC 247191522.
- .
- ISSN 0947-5117.
- OCLC 40857022.
- ISSN 1528-7483.
- PMID 24482834.
- hdl:10261/130728. Archivedfrom the original on 2015-09-07.
- OCLC 48554849
- OCLC 1241842166.
- ^ "The Nobel Prize in Physics 1914". Nobel Foundation. Retrieved 2008-10-09.
- ^ "The Nobel Prize in Physics 1915". Nobel Foundation. Retrieved 2008-10-09.
- ^ "The Nobel Prize in Chemistry 1962". Nobelprize.org. Retrieved 2008-10-06.
- ^ "The Nobel Prize in Physiology or Medicine 1962". Nobel Foundation. Retrieved 2007-07-28.
- ^ "The Nobel Prize in Chemistry 1964". Nobelprize.org. Retrieved 2008-10-06.
- ^ "The Nobel Prize in Chemistry 1972". Nobelprize.org. Retrieved 2008-10-06.
- ^ "The Nobel Prize in Chemistry 1976". Nobelprize.org. Retrieved 2008-10-06.
- ^ "The Nobel Prize in Chemistry 1985". Nobelprize.org. Retrieved 2008-10-06.
- ^ "The Nobel Prize in Chemistry 1988". Nobelprize.org. Retrieved 2008-10-06.
- ^ "The Nobel Prize in Chemistry 1997". Nobelprize.org. Retrieved 2008-10-06.
- ^ a b "The Nobel Prize in Chemistry 2003". Nobelprize.org. Retrieved 2008-10-06.
- ^ "The Nobel Prize in Chemistry 2006". Nobelprize.org. Retrieved 2008-10-06.
- ^ "The Nobel Prize in Chemistry 2009". Nobelprize.org. Retrieved 2009-10-07.
- ^ "The Nobel Prize in Chemistry 2012". Nobelprize.org. Retrieved 2012-10-13.
Further reading
International Tables for Crystallography
- Hahn T, ed. (2002). International Tables for Crystallography. Volume A, Space-group Symmetry (5th ed.). Dordrecht: ISBN 0-7923-6590-9.
- Rossmann MG, Arnold E, eds. (2001). International Tables for Crystallography. Volume F, Crystallography of biological molecules. Dordrecht: Kluwer Academic Publishers, for the International Union of Crystallography. ISBN 0-7923-6857-6.
- Hahn T, ed. (1996). International Tables for Crystallography. Brief Teaching Edition of Volume A, Space-group Symmetry (4th ed.). Dordrecht: Kluwer Academic Publishers, for the International Union of Crystallography. ISBN 0-7923-4252-6.
Bound collections of articles
- Carter Jr CW, Sweet RM, eds. (1997). Macromolecular Crystallography, Part A (Methods in Enzymology, v. 276). San Diego: Academic Press. ISBN 0-12-182177-3.
- Carter Jr CW, Sweet RM, eds. (1997). Macromolecular Crystallography, Part B (Methods in Enzymology, v. 277). San Diego: Academic Press. ISBN 0-12-182178-1.
- Ducruix A, Giegé R, eds. (1999). Crystallization of Nucleic Acids and Proteins: A Practical Approach (2nd ed.). Oxford: Oxford University Press. ISBN 0-19-963678-8.
Textbooks
- Birkholz M, Fewster PF, Genzel C (2005). "Chapter 1: Principles of X-ray Diffraction". Thin Film Analysis by X-Ray Scattering. Weinheim: Wiley-VCH. ISBN 978-3-527-31052-4– via ResearchGate.
- Blow D (2002). Outline of Crystallography for Biologists. Oxford: Oxford University Press. ISBN 0-19-851051-9.
- Burns G, Glazer AM (1990). Space Groups for Scientists and Engineers (2nd ed.). Boston: Academic Press, Inc. ISBN 0-12-145761-3.
- Clegg W (1998). Crystal Structure Determination (Oxford Chemistry Primer). Oxford: Oxford University Press. ISBN 0-19-855901-1.
- Cullity BD (1978). Elements of X-Ray Diffraction (2nd ed.). Reading, Massachusetts: Addison-Wesley Publishing Company. ISBN 0-534-55396-6.
- Drenth J (1999). Principles of Protein X-Ray Crystallography. New York: Springer-Verlag. ISBN 0-387-98587-5.
- Giacovazzo C (1992). Fundamentals of Crystallography. Oxford: Oxford University Press. ISBN 0-19-855578-4.
- Glusker JP, Lewis M, Rossi M (1994). Crystal Structure Analysis for Chemists and Biologists. New York: VCH Publishers. ISBN 0-471-18543-4.
- Massa W (2004). Crystal Structure Determination. Berlin: Springer. ISBN 3-540-20644-2.
- McPherson A (1999). Crystallization of Biological Macromolecules. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. ISBN 0-87969-617-6.
- McPherson A (2003). Introduction to Macromolecular Crystallography. John Wiley & Sons. ISBN 0-471-25122-4.
- McRee DE (1993). Practical Protein Crystallography. San Diego: Academic Press. ISBN 0-12-486050-8.
- O'Keeffe M, Hyde BG (1996). Crystal Structures; I. Patterns and Symmetry. Washington, DC: Mineralogical Society of America, Monograph Series. ISBN 0-939950-40-5.
- Rhodes G (2000). Crystallography Made Crystal Clear (PDF). San Diego: Academic Press. ISBN 0-12-587072-8– via UW-Eau Claire, Chem 406, Fall 2005.
- Rupp B (2009). Biomolecular Crystallography: Principles, Practice and Application to Structural Biology. New York: Garland Science. ISBN 978-0-8153-4081-2.
- Warren BE (1969). X-ray Diffraction. New York: Dover Publications. ISBN 0-486-66317-5.
- Zachariasen WH (1945). Theory of X-ray Diffraction in Crystals. New York: Dover Publications. LCCN 67026967.
Applied computational data analysis
- Young RA, ed. (1993). The Rietveld Method. Oxford: Oxford University Press & International Union of Crystallography. ISBN 0-19-855577-6.
Historical
- Bijvoet MJ, Burgers WG, Hägg G, eds. (1969). Early Papers on Diffraction of X-rays by Crystals. Vol. I. Utrecht: published for the International Union of Crystallography by A. Oosthoek's Uitgeversmaatschappij N.V.
- Bijvoet JM, Burgers WG, Hägg G, eds. (1972). Early Papers on Diffraction of X-rays by Crystals. Vol. II. Utrecht: published for the International Union of Crystallography by A. Oosthoek's Uitgeversmaatschappij N.V.
- Bragg WL, Phillips DC, Lipson H (1992). The Development of X-ray Analysis. New York: Dover. ISBN 0-486-67316-2.
- ISBN 978-1-4615-9963-0.
- Ewald PP (ed.). "50 Years of X-Ray Diffraction". International Union of Crystallography.
Reprinted in pdf format for the IUCr XVIII Congress, Glasgow, Scotland
- Friedrich W (1922). "Die Geschichte der Auffindung der Röntgenstrahlinterferenzen". Die Naturwissenschaften. 10 (16): 363. S2CID 28141506.
- Lonsdale K (1949). Crystals and X-rays. New York: D. van Nostrand.
External links
Tutorials
- Learning Crystallography
- Simple, non technical introduction
- The Crystallography Collection, video series from the Royal Institution
- "Small Molecule Crystalization" (PDF) at Illinois Institute of Technology website
- International Union of Crystallography
- Crystallography 101
- Interactive structure factor tutorial, demonstrating properties of the diffraction pattern of a 2D crystal.
- Picturebook of Fourier Transforms, illustrating the relationship between crystal and diffraction pattern in 2D.
- Lecture notes on X-ray crystallography and structure determination
- Online lecture on Modern X-ray Scattering Methods for Nanoscale Materials Analysis by Richard J. Matyi
- Interactive Crystallography Timeline Archived 2021-06-30 at the Wayback Machine from the Royal Institution
Primary databases
- Crystallography Open Database(COD)
- Protein Data Bank (PDB)
- Nucleic Acid Databank (NDB)
- Cambridge Structural Database (CSD)
- Inorganic Crystal Structure Database (ICSD)
- Biological Macromolecule Crystallization Database (BMCD)
Derivative databases
- PDBsum
- Proteopedia – the collaborative, 3D encyclopedia of proteins and other molecules
- RNABase
- HIC-Up database of PDB ligands Archived 2020-08-08 at the Wayback Machine
- Structural Classification of Proteinsdatabase
- CATH Protein Structure Classification
- List of transmembrane proteins with known 3D structure Archived 2011-04-11 at the Wayback Machine
- Orientations of Proteins in Membranes database
Structural validation
- MolProbity structural validation suite
- ProSA-web
- NQ-Flipper (check for unfavorable rotamers of Asn and Gln residues)
- DALI server (identifies proteins similar to a given protein)