The Link to X-Ray Protein Crystallography


A. Crystal Production

(wet lab)

  1. Production
  2. Purification
  3. Crystallisation

 

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B. Data Collection

(x-ray lab)

  1. Mounting
  2. Shooting
  3. Detection

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C. Structure Solution

(computer lab)

  1. Indexing
  2. Integration
  3. Scaling
  4. Phasing
  5. Building
  6. Refinement
  7. Validation
  8. Publication

Indexing

Two seperate pieces of information can be found in the reflections of the diffraction images. The first comes from the geometrical arrangement of the reflections, which gives all the information about the crystal lattice and the symmetry of the crystal. The second comes from the intensity of the reflection that gives part of the information about the content of the lattice. Unfortunately the second kind, which is the one that we are actually interested in, is only partial - we lack the phases. During indexing the spots have to be found, named with integer numbers (h, k, l = Miller Indices) and the crystal geometry has to be determined accurately so that the intensities can be integrated accurately and that the space that has to be modelled later on is defined accurately.

Labeled diffraction pattern with Miller indices (hkl)

The unit cell is the smallest bit in a crystal that can simply be stacked onto the next unit cell by simple translation to reconstitute the whole crystal. There are few possible shapes (crystal systems) of unit cells that can make a crystal. The primitive unit cell contains one repeating motive per unit cell, but the motive is often present more than once per unit cell wich leads to higher symmetry. This extension by symmetry leads to the so called Bravais lattices. A unit cell is defined by three distances (a, b, c) and three angles (α, β, γ).

The asymetric unit ultimately is the smallest possible bit that can be repeated in space to reconstitute the whole crystal. It can contain more than one protein. One motives in the Bravais lattice can be made of more than one asymmetric unit. The symmery relations between the asymetric units of chiral molecules within a crystal motive involve only simple rotations and rotations around a screw axis (rotation combined with translation).The only possible rotations in a crystal are 1, 2, 3, 4, 6-fold. The only possible screw axis are 21, 31, 32, 41, 42, 43, 61, 62, 63, 64, 65 (where the first number is the rotation and the second number divided by the first is the translation in part of the unit cell). 43 means a 90° rotation combined with a 3/4 of the unit cell length translation which results in the fourth asymmetric unit to be located in the next unit cell. The simplest and most general crystal would be P1 with one molecule in the asymmetric unit.

Crystal systems
(7 possible)

Bravais lattices
(14 possible)
P, C, I, F, R
primitive, base centered, body centered, face centered, rhombohedral

Space groups
(65 possible for chiral molecules)
Simple rotations:
1, 2, 3, 4, 6-fold (= by 360, 180, 120, 90, 60°)
Screw axis:
21, 31, 32, 41, 42, 43, 61, 62, 63, 64, 65
(nz: n-fold rotation + z/n unit cell length translation)

Triclinic P P 1
Monoclinic P C

P 2 / P 21

C 2

Orthorhombic P C I F

P 2 2 2 / P 2 2 21 / P 21 21 2 / P 21 21 21

C 2 2 21 / C 2 2 2

I 2 2 2 / I 21 21 21

F 2 2 2

Trigonal
(or Rhombohedral)
P R

P 3 / P 31 / P 32
P 3 1 2 / P 3 2 1
P 31 1 2 / P 31 2 1
P 32 1 2 / P 32 2 1

R 3 / R 3 2

Tetragonal P I

P 4 / P 41 / P 42 / P 43
P 4 2 2 / P 4 21 2 / P 41 2 2 / P 41 21 2
P 42 2 2 / P 42 21 2
P 43 2 2 / P 43 21 2

I 4 / I 41
I 4 2 2 / I 41 2 2 

Hexagonal
(special kind of Trigonal)
P P 6 / P 61 / P 62 / P 63 / P 64 / P 65
P 6 2 2 / P 61 2 2 / P 62 2 2 / P 63 2 2 / P 64 2 2 / P 65 2 2
Cubic P I F

P 2 3 / P 21 3
P 4 3 2 / P 41 3 2 / P 42 3 2 / P 43 3 2

I 2 3 / I 21 3 / I 4 3 2 / I 41 3 2

F 2 3 / F 4 3 2 / F 41 3 2

Crystal systems, Bravais lattices and chiral space groups. The black dot represents one point per repeated motive.

Primitive orthorombic unit cell with three 21 symmetry axis = P 21 21 21, the most commen space group for proteins. Each asymmetric unit consists of one single molecule in this case.

LINKS

Crystallography 101
CRYSTOSIM
Space Group Diagrams and Tables (all 230)

PROGRAMMES

MOSFLM, indexing, integration
HKL2000, indexing, integration


Mission / Organisations / Trivia / Links / Florian Fisch / 5 June 2009