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Structural Biology Summary for the first Reading:

UnitCell:Undercertaincircumstances,manymolecularsubstances,includingproteins,
solidifytoformcrystals.Inenteringthecrystallinestatefromsolution,individual
moleculesofthesubstanceadoptoneorafewidenticalorientations.Theresulting
crystalisanorderlythreedimensionalarrayofmolecules,heldtogetherbynoncovalent
interactions.Figure2.4depictssuchacrystallinearrayofmolecules.
Thelinesinthefiguredividethecrystalintoidenticalunitcells.Thearrayofpointsatthe
cornersorverticesofunitcellsiscalledthelattice.Theunitcellisthesmallestand
simplestvolumeelementthatiscompletelyrepresentativeofthewholecrystal.Ifwe
knowtheexactcontentsoftheunitcell,wecanimaginethewholecrystalasan
efficientlypackedarrayofmanyunitcellsstackedbesideandontopofeachother,more
orlesslikeidenticalboxesinawarehouse.(Page31)
Resolution:Alternatively,actualdistances,ratherthanreflectionindices,canbe
measuredinreciprocalspace.Becausethedimensionsofreciprocalspacearetheinverse
ofdimensionsintherealspaceofthecrystal,distancesinreciprocalspaceareexpressed
intheunits1(calledreciprocalangstroms).Roughlyspeaking,theinverseofthe
reciprocalspacedistancefromtheoriginouttothemostdistantmeasurablereflections
givesthepotentialresolutionofthemodelthatwecanobtainfromthedata.Soacrystal
thatgivesmeasurablereflectionsouttoadistanceof1/(3)fromtheoriginissaidto
yieldamodelwitharesolutionof3.
Crystallographersworkbackandforthbetweentwodifferentcoordinatesystems.Iwill
reviewthembriefly.Thefirstsystem(seeFig.2.5,p.12)istheunitcell(realspace),
whereanatomspositionisdescribedbyitscoordinatesx,y,z.Avertexoftheunitcell,
oranyotherconvenientposition,istakenastheorigin,withcoordinatesx,y,z=(0,0,
0).Coordinatesinrealspacedesignaterealspatialpositionswithintheunitcell.Real
spacecoordinatesareusuallygiveninangstromsornanometers,orinfractionsofunit
celldimensions.Thesecondsystem(seeFig.2.12,p.19)isthethreedimensional
diffractionpattern(reciprocalspace),whereareflectionspositionisdescribedbyits
indiceshkl.Thecentralreflectionistakenastheoriginwiththeindexhkl=000(round
blackdotatcenterofsphere).Thepositionofareflectionisdesignatedbycounting
reflectionsfrom000,sotheindicesh,k,andlareintegers.Distancesinreciprocal
space,expressedinreciprocalangstroms(1)orreciprocalnanometers(nm1),areused
tojudgethepotentialresolutionofthemodelthatthediffractiondatacanyield.
StructureFactor:EachdiffractedXraythatarrivesatthefilmtoproducearecorded
reflectioncanalsobedescribedasthesumofthecontributionsofallscatterersintheunit
cell.Thesumthatdescribesadiffractedrayiscalledastructurefactorequation.The

computedsumforthereflectionhkliscalledthestructurefactorFhkl.AsIwillshowin
Chapter4,thestructurefactorequationcanbewritteninseveraldifferentways.For
example,oneusefulformisasuminwhicheachtermdescribesdiffractionbyoneatom
intheunitcell,andthusthesumcontainsthesamenumberoftermsasthenumberof
atoms.
IfdiffractionbyatomAinFig.2.17isrepresentedbyfA,thenonediffractedray
(producingonereflection)fromtheunitcellofFig.2.17isdescribedbyastructurefactor
equationofthisform:
Fhkl=fA+fB++fA+fB++fF.(2.3)
Thestructurefactorequationimplies,andcorrectlyso,thateachreflectiononthefilmis
theresultofdiffractivecontributionsfromallatomsintheunitcell.Thatis,everyatom
intheunitcellcontributestoeveryreflectioninthediffractionpattern.Thestructure
factorFhklisawavecreatedbythesuperpositionofmanyindividualwavesfj,each
resultingfromdiffractionbyanindividualatom.Sothestructurefactoristhesumof
manywaveequations,onefordiffractionbyeachatom.Inthatsense,thestructurefactor
equationisaFouriersum(sometimescalledaFouriersummation,butIpreferone
syllabletothree),butnotaFourierseries.InaFourierseries,eachsucceedingtermcan
begeneratedfromthepreviousonebysomerepetitiveformula,asinFig.2.16.
Reflections:Figure2.6depictsthecollectionofXraydiffractiondata.Acrystalis
mountedbetweenanXraysourceandanXraydetector.Thecrystalliesinthepathofa
narrowbeamofXrayscomingfromthesource.ThesimplestsourceisanXraytube,
andthesimplestdetectorisXrayfilm,whichwhendevelopedexhibitsdarkspotswhere
Xraybeamshaveimpinged.Thesespotsarecalledreflectionsbecausetheyemergefrom
thecrystalasifreflectedfromplanesofatoms.
Anopticalscannerpreciselymeasuresthepositionandtheintensityofeachreflection
andtransmitsthisinformationindigitalformtoacomputerforanalysis.Thepositionof
areflectioncanbeusedtoobtainthedirectioninwhichthatparticularbeamwas
diffractedbythecrystal.Theintensityofareflectionisobtainedbymeasuringtheoptical
absorbanceofthespotonthefilm,givingameasureofthestrengthofthediffracted
beamthatproducedthespot.Thecomputerprogramthatreconstructsanimageofthe
moleculesintheunitcellrequiresthesetwoparameters,therelativeintensityand
direction,foreachdiffractedbeamthatproducesareflectionatthedetector.Theintensity
issimplyanumberthattellshowdarkthereflectionisincomparisontotheothers.The
beamdirection,asIwilldescribeshortly,isspecifiedbyasetofthreedimensional
coordinatesh,k,andlforeachreflection.