Physical Biochemistry X-Ray Crystallography 2
Properties of Crystals and Crystal Symmetry:
Good Crystals
Diffract X-rays to reasonably high resolution (at least 3 Å)
Diffracts in 3 dimensions – Isotropic diffraction
Single (not twinned, split or attached to another crystal)
Reproducible
Stable
Appearance is unimportant
A crystal is an ordered array of molecules
Solvent content: 25-90%
Molecules are linked by
Ionic interactions
H-bonds
Hydrophobic interactions
To study positions of all atoms we have to have a set of reference aces and an origin
This creates a box around the molecule – known as the
unit cell
The unit cell is defined as containing at least one repeating unit of
the crystal within it
The crystal can be reconstructed by translating the unit cell by
multiples of the axes lengths a, b, c.
a, b, c = lengths of the unit cell edges [Å]
(b & c), (a & c), (a & b) = angles between the edges
These parameters are measured from the data
7 Crystal systems – all are mathematically defined
Triclinic
Monoclinic
Orthorhombic
Tetragonal
Trigonal
Hexagonal
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Physical Biochemistry X-Ray Crystallography 2
Cubic
There can often be more than one molecule / unit cell
Asymmetric unit is the smallest unit from which the crystal can be created by applying crystal
symmetry operations (rotations & translations) to create the unit cell.
A two-fold rotation of the asymmetric unit
will create the unit cell shown on the right.
An object has symmetry if symmetry operations can be applied that leave the
object indistinguishable from the object in its original orientation.
Rotations or translations do not change the ‘hand’ of an object, inversions or
reflections will.
A pair of molecules with different ‘hands’ are known as enantiomorphs
Proteins are composed only of L-amino acids; only rotations and translations
are allowed in protein crystals – mirror plane symmetry is not involved (which is
good because its very complicated)
Space Group of a crystal is a description of crystal symmetry relating
to the molecules within the unit cell. Each asymmetric unit within the
unit cell is related to others in the unit cell by symmetry operations.
Pure rotations – rotations only, e.g. 2-fold 180 rotation
Screw axes – rotations combined with translation
o 21 screw axis = 180, then translate ½ unit cell dimension
Centring – a 2nd repeating unit on 1 or more faces of the crystal
Several of these symmetry elements exist in the unit cell, giving rise to
complex space group definitions
e.g. P212121 – Primitive lattice, a 21 screw axis in each dimension
Centring
Primitive (P) lattice: one lattice point at each corner
I: extra lattice point at the centre of the unit cell
Face centred (F): an extra lattice point at the centre of the unit cell
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Physical Biochemistry X-Ray Crystallography 2
A, B, C centred: an extra copy on one face
Pure rotational symmetry
No symmetry: P1
2-fold rotation: P2
4-fold rotation: P4
There are a total of 230 space groups, however only 65 of these occur in proteins and large
biomolecules because these molecules are chiral – mirror planes are not possible.
Symmetry is important, as the symmetry of a crystal affects the diffraction pattern
Symmetry axes within a crystal will lead to symmetry in the diffraction pattern
Some diffraction spots will be the same, as they are related by symmetry, and can be averaged
If symmetry can be described of all the molecules in a unit cell, the atom positions do not all need
to be described.
The number of parameters (X,Y,Z coordinates) required to describe structure is 3 × the number of
atoms. If unit cells contains 2 asymmetric units, then you only need half of this.
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