Lecture2: CrystalSymmetry

Crystalsaremadeofinfinitenumberofunitcells
Unitcellisthesmallestunitofacrystal,which,if
repeated,couldgeneratethewholecrystal.

Acrystalsunitcelldimensionsaredefinedbysixnumbers,
thelengthsofthe3axes,a,b,andc,andthethreeinteraxial
angles,,and.

Acrystallatticeisa3Dstackofunitcells

Crystallatticeisanimaginativegridsysteminthreedimensionsin
whicheverypoint(ornode)hasanenvironmentthatisidenticaltothat
ofanyotherpointornode.

Millerindices
AMillerindexisaseriesofcoprimeintegersthatareinversely
proportionaltotheinterceptsofthecrystalfaceor
crystallographicplaneswiththeedgesoftheunitcell.
Itdescribestheorientationofaplaneinthe3Dlatticewith
respecttotheaxes.
ThegeneralformoftheMillerindexis(h,k,l)whereh,k,andl
areintegersrelatedtotheunitcellalongthea,b,ccrystalaxes.

MillerIndices
RulesfordeterminingMillerIndices:

1.Determinetheinterceptsoftheface
alongthecrystallographicaxes,in
termsofunitcelldimensions.
2.Takethereciprocals
3.Clearfractions
4.Reducetolowestterms
An example of the (111) plane (h=1,
k=1, l=1) is shown on the right.

Anotherexample:
RulesfordeterminingMillerIndices:
1.Determinetheinterceptsoftheface
alongthecrystallographicaxes,in
termsofunitcelldimensions.
2.Takethereciprocals
3.Clearfractions
4.Reducetolowestterms

WheredoesaproteincrystallographerseetheMillerindices?
Commoncrystalfacesare
paralleltolatticeplanes

Eachdiffractionspotcanbe

regardedasaXraybeam
reflectedfromalatticeplane,
andthereforehasaunique
Millerindex.

Symmetry
Astateinwhichpartsonoppositesidesofaplane,
line,orpointdisplayarrangementsthatarerelatedto
oneanotherviaasymmetryoperationsuchas
translation,rotation,reflectionorinversion.
Applicationofthesymmetryoperatorsleavesthe
entirecrystalunchanged.

SymmetryElements
Rotation
turns all the points in the asymmetric
unit around one axis, the center of
rotation. A rotation does not change
the handedness of figures. The center
of rotation is the only invariant point
(point that maps onto itself).

Symmetryelements:rotation

Symmetryelements:rotation

SymmetryElements
Translation

moves all the points in the

asymmetric unit the same
distance in the same direction.
This has no effect on the
handedness of figures in the
plane. There are no invariant
points (points that map onto
themselves) under a translation.

SymmetryElements
Screw axes (rotation + translation)
rotation about the axis of
symmetry by 360/n, followed
by a translation parallel to the
axis by r/n of the unit cell length
in that direction. (r < n)

120rotation
1/3unitcelltranslation

SymmetryElements
Inversion,orcenterofsymmetry
everypointononesideof
acenterofsymmetryhasa
similarpointatanequal
distanceontheopposite
sideofthecenterof
symmetry.

SymmetryElements
MirrorplaneorReflection
flips all points in the asymmetric unit
over a line, which is called the mirror,
and thereby changes the handedness of
any figures in the asymmetric unit.
The points along the mirror line
are all invariant points (points that map
onto themselves) under a reflection.

Symmetryelements:
mirrorplaneandinversioncenter

Thehandednessischanged.

SymmetryElements
Glide reflection (mirror plane + translation)
reflects the asymmetric unit
across a mirror and then
translates parallel to the mirror.
A glide plane changes the
handedness of figures in the
asymmetric unit. There are no
invariant points (points that map
onto themselves) under a glide
reflection.

Symmetriesincrystallography

Crystalsystems
Latticesystems
Spacegroupsymmetry
Pointgroupsymmetry
Lauesymmetry,Pattersonsymmetry

Crystalsystem
Crystalsaregroupedintosevencrystal
systems,accordingtocharacteristic
symmetryoftheirunitcell.
Thecharacteristicsymmetryofacrystalisa
combinationofoneormorerotationsand
inversions.

7CrystalSystems
cubic

monoclinic

orthorhombic
tetragonal

triclinic

trigonal

Crystal System

External Minimum Symmetry

Triclinic
Monoclinic
Orthorhombic
Tetragonal
Trigonal
Hexagonal
Cubic

None
a, b, c, al, be, ga,
One 2-fold axis, || to b (b unique)
a, b, c, 90, be, 90
Three perpendicular 2-foldsa, b, c, 90, 90, 90
One 4-fold axis, parallel c
a, a, c, 90, 90, 90
One 3-fold axis
a, a, c, 90, 90, 120
One 6-fold axis
a, a, c, 90, 90, 120
Four 3-folds along space diagonal
a, a, ,a, 90, 90, 90

hexagonal

Unit Cell Properties

AugusteBravais
(18111863)

Lattices

In1848,AugusteBravaisdemonstratedthat
ina3dimensionalsystemtherearefourteen
possiblelattices
ABravaislatticeisaninfinitearrayof
discretepointswithidenticalenvironment
sevencrystalsystems+fourlatticecentering
types=14Bravaislattices
Latticesarecharacterizedbytranslation
symmetry

Fourlatticecenteringtypes
No.

Type

Description

Primitive

Latticepointsoncorners
only.Symbol:P.

FaceCentered

Latticepointsoncornersas
wellascenteredon
faces.Symbols:A(bc
faces);B(acfaces);C
(abfaces).

AllFaceCentered

Latticepointsoncornersas
wellasinthecentersof
allfaces.Symbol:F.

BodyCentered

Latticepointsoncornersas
wellasinthecenterof
theunitcellbody.
Symbol:I.

Tetragonallatticesareeitherprimitive(P)or
bodycentered(I)
Ccenteredlattice
=
Primitivelattice

Monocliniclatticesareeitherprimitive
orCcentered

Pointgroupsymmetry
Inorganiccrystalsusuallyhaveperfectshape
whichreflectstheirinternalsymmetry
Pointgroupsareoriginallyusedtodescribethe
symmetryofcrystal.
Pointgroupsymmetrydoesnotconsider
translation.
Includedsymmetryelementsarerotation,mirror
plane,centerofsymmetry,rotaryinversion.

Pointgroupsymmetrydiagrams

Thereareatotal
of32pointgroups

Nfoldaxeswithn=5orn>6does
notoccurincrystals

Adjacentspacesmustbecompletelyfilled(nogaps,no
overlaps).

Laueclass,Pattersonsymmetry
Laueclasscorrespondstosymmetryof
reciprocalspace(diffractionpattern)
PattersonsymmetryisLaueclassplus
allowedBravaiscentering(Pattersonmap)

Spacegroups
The combination of all available symmetry operations (32
point groups), together with translation symmetry,
within the all available lattices (14 Bravais lattices) lead
to 230 Space Groups that describe the only ways in which
identical objects can be arranged in an infinite lattice.
The International Tables list those by symbol and
number, together with symmetry operators, origins,
reflection conditions, and space group projection
diagrams.

AdiagramfromInternationalTableofCrystallography

IdentificationoftheSpaceGroupiscalledindexingthecrystal.
TheInternationalTablesforXrayCrystallographytellusahuge
amountofinformationaboutanygivenspacegroup.Forinstance,
IfwelookupspacegroupP2,wefindithasa2foldrotationaxis
andthefollowingsymmetryequivalentpositions:
X
-X

,
,

Y
Y

, Z
, -Z

andanasymmetricunitdefinedby:
0x1
0y1
0z1/2
AninteractivetutorialonSpaceGroupscanbefoundonlineinBernhardRupps
Crystallography101Course:http://wwwstructure.llnl.gov/Xray/tutorial/spcgrps.htm

SpacegroupP1

Pointgroup1+BravaislatticeP1

SpacegroupP1bar

Pointgroup1bar+BravaislatticeP1

SpacegroupP2

Pointgroup2+Bravaislatticeprimitivemonoclinic

SpacegroupP21

Pointgroup2+Bravaislatticeprimitivemonoclinic,
butconsiderscrewaxis

Coordinatetriplets,equivalentpositions

r=ax+by+cz,
Therefore,eachpointcanbedescribedbyitsfractional
coordinates,thatis,byitscoordinatetriplet(x,y,z)

Spacegroupdetermination
Symmetryindiffractionpattern
Systematicabsences
Spacegroupswithmirrorplanesand
inversioncentersdonotapplytoprotein
crystals,leavingonly65possiblespace
groups.

AlessoninsymmetryfromM.C.Escher

Anotherone:

Asymmetricunit
Recallthattheunitcellofacrystalisthesmallest3Dgeometric
figurethatcanbestackedwithoutrotationtoformthelattice.The
asymmetricunitisthesmallestpartofacrystalstructurefrom
whichthecompletestructurecanbebuiltusingspacegroup
symmetry.Theasymmetricunitmayconsistofonlyapartofa
molecule,oritcancontainmorethanonemolecule,ifthemolecules
notrelatedbysymmetry.

MatthewCoefficient
Matthewsfoundthatformanyproteincrystalsthe
ratiooftheunitcellvolumeandthemolecular
weightisbetween1.7and3.53/Dawithmost
valuesaround2.153/Da
Vmisoftenusedtodeterminethenumberof
moleculesineachasymmetricunit.
Noncrystallographicsymmetryrelatedmolecules
withintheasymmetricunit