# 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.

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## Abbreviations

* Å: Angstrom, unit of distance (1Å = 10nm = 1x10$^{-10}$m)
* a.s.u.: Asymmetric Unit
* c: speed of light in a vacuum ( 299,792,458 meters per second or aprox. 3x10$^8$m/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$^{-9}$m)
* 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