Xray Crystallography/Introduction

Introduction

X-ray crystallography is a powerful technique for visualising the structure of protein. X-rays are directed onto a crystal where the rays diffract from planes within the crystal in accordance with Braggs law. The resulting diffraction pattern can then be collected. The positions of the spots in the diffraction pattern give information about the structure of the crystal. However not all of the information about the crystal is collected by the recording equipment, spot intensities can be measured but the phase information is lost, resulting in a phase ambiguity. There are many techniques used to extract the phase information from the crystal in other ways, for small molecules the phase can be solved directly using a Patterson map, for more complex molecules phases from a similar structure can be used, or phase information can be extracted from anomalous scatters. In all cases a model is calculated from the observed structure factors and the calculated phases, this model is then refined to fit the model to the data.

Why a Wikibook?

So why write or use a Wikibook? Much with the success of [CCP4], where many crystallographers around the world have contributed code freely to the community and in return everyone can enjoy a whole suite of programs, the same can be true of a Wikibook. If everyone maintained one section, then for a small amount of work you can share in a whole textbook for free. With a little maintenance here and there the book will always be up to date. If enough people get involved it will be peer-review at its best.

How to Help

There are many ways in which you can help this Wikibook. If you can see a mistake - correct it! If you feel the book is missing an important topic - then write it, or if you cannot, suggest it on the talk page. The book may need grammatical or spelling corrections, new illustrative images are always welcome. If you feel you can write about an advanced topic outside the scope of this book, such as formula derivations or details on specific equipment, then add in an appendix or write an article in Wikipedia and link to it.

Abbreviations

Å: Angstrom, unit of distance (1Å = 10nm = 1x10^-10m)
a.s.u.: Asymmetric Unit
c: speed of light in a vacuum ( 299,792,458 meters per second or aprox. 3x10⁸m/s)
CC: Correlation coefficient
CCD: Charge-Coupled Device
CCP4: [Collaborative Computer Project number 4]
Cryo: Cryogenic temperature, at or below 77K (temperature of liquid Nitrogen)
Da: Dalton
EDTA: Ethylenediaminetetraacetic acid
eV: electron-volt, unit of energy, It is the amount of kinetic energy gained by a single unbound electron
EXAFS: Extended X-ray Absorption Fine Spectra
FOM: Figure Of Merit
GUI: Graphical User Interface
Gy: Gray, Unit of dose, (1 Gy = 1 J•kg^-1)
h: Planck's constant (6.626 × 10^-34 J•s)
HEPES: 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
HEWL: Hen Egg-White Lysozyme
K: Kelvin
kDa: kiloDalton
keV: kilo-electron Volt
M: Molar concentration
MAD: Multiple-wavelength Anomalous Dispersion
MIR: Multiple Isomorphous Replacement
MIRAS: Multiple Isomorphous Replacement with Anomalous Scattering
MPD: 2-methyl-2,4-pentanediol
MX: Macromolecular Crystallography
NaAc: Sodium Acetate
nm: Nanometre, unit of distance (1nm = 1x10^-9m)
NMR: Nuclear Magnetic Resonance
pA: pico Amps (current)
pdb: [RCSB Protein Data Bank]
PEG: Polyethylene Glycol
PX: Protein Crystallography
RCSB: Research Collaboratory for Structural Bioinformatics
RIP: Radiation-damage Induced Phasing
RIPAS: Radiation-damage Induced Phasing with Anomalous Scattering
RMSD: Root Mean Square Deviation
SAD: Single-wavelength Anomalous Dispersion
Se-Met: Selenomethionine
SIR: Single Isomorphous Replacement
SIRAS: Single Isomorphous Replacement with Anomalous Scattering
Tris: Tris (hydroxymethyl) aminomethane buffer
v/v: Volume by volume
w/v: Weight by volume