Lec 2 Overview

Question 1

What are the first three steps of x ray crystallography

Answer 1

Obtain crystals

Collect data

Obtain phases

Question 2

What does the wavelength have to be in

Regular light microscopy

x ray crystallography

Answer 2

Both have to be less then the length of the object so the object can be dicerened

Visible light:
- 400-700nm

X-ray:
- 0.1-100 A, usually around 1A
- 1A bc the bond on C backbone are 1.5A, allow us to discern images of atoms
- show interactions with electrons , biggest ineraction with more e-, least with H bc only 1e-

Question 3

How is the setup of x ray crystallography diff from light microscopy

Answer 3

Source : x rays

Object: crystal

Detected is used , there are no lenses

The reconstructed image is e- density :
- give contour lines where highest e- density is in centre

Question 4

What is the x ray source

Answer 4

Synchrotron

Question 5

What is a unit cell

Translationally symmetry

Lattice and node

Answer 5

Unit cell: Element is translated through three dimensions to give the crystal

TS: sliding across x axis

Lattice and node: lattice is array of line ld that makes up the boxes, nodes are points that form the lattice

Question 6

What is special about the symmetry in the crystal and what does it allow us to do

Answer 6

Only need the description of one molecule and the symmetry to describe the entire crystal

Meaning can describe other object in the crystals if you know one of the objects already

Question 7

Describe the coordinates in a model in a crystal

What types of symmetry are there in the crystal

Answer 7

Define the positions of the atom by x,y,z atomic coordinates

Symmetry related atoms on the neighbouring unit cells

Symmetry related atoms in the same unit cell

Question 8

Describe the electron density map

Answer 8

The electron density map is contoured at a single specific level above the boise level

then the model is fitted into the electron density according to interpretations by crystallographer

Question 9

Describe the film in the x ray diffraction exponent once the crystal diffracts the x rays

Answer 9

The diffracted rays cause darkness on the film called “reflections”

More intense, bigger reflection

Centre is blank because of the beam stop (don’t want direct x ray beam bc that damages the detector

The dat you get from the film is the intensity and the position (where the reflections land on the detector/film

Question 10

Describe the trend of the diffraction pattern

Answer 10

Dark centre, fades at the sides, the reciprocal of the atom in the crystal

Any symmetry in the atom/molecule is retained in the diffraction pattern.

if in an array, there’s no more symmetry so the diff reaction pattern doesn’t have symmetry anymore

Question 11

What are the coordinates for reflections

For the atoms that give those reflections

Answer 11

h,k,l

X,y,z

Question 12

What does table 1 in a crystallographic paper show

Answer 12

Describes the crystallographic data

States how well the crystals diffract

Might describe only one data set

Question 13

What is a Fourier transform in crystallography

Answer 13

Combines info from the diffraction pattern to simulate a lens (bc we don’t actually have a lens in x ray crystallography) and reconstruct the electron density

What it gives is a set of structure factors (Fhkl) which are used to calculate the electron density at each position in real space:

• p(x,y,z)
• rho is electron density

Question 14

Slode 20

Answer 14

The computer which transforms the data stimulates the lens

All transformation are happening via the computer which why this process is a black box (don’t actually know what’s happening inside it)

Question 15

Each diffracted x ray is

Explain the structure factor

Answer 15

The sum of the contributions from all atoms in the unit cell

Structure factors (Fhkl)
- the sum of those contributions from those atoms (so the reflection caused by the diffracted ray)
- ex. Fhkl= fA +fB + fA’ + …
- these are vectors so write the in bold or half arrow

• in other word the structure factor is a fourier sum: wave created by addition of waves from individual atoms

Question 16

What is electron density and how does it come about

Answer 16

Because electrons diffract x rays, the diffraction reveals the electron density

p(x,y,z)

Then a contour map is calculated from the electron density to make it interpretable

Then, if amplitude frequency and phases of each reflection are known, the Fourier transform will take us between Fhkl (reflections) and p(xyz) (electron density)

Question 17

What does the intensity of a reflection give

Answer 17

Amplitude

Question 18

What does the diffraction pattern give us

Answer 18

The positions of the reflections

Intensities of the reflections

But does not give phases

Question 19

How do we get phases

Answer 19

Look for the orientation and position of a similar molecule in a crystal

Soak heavy atoms into crystals

Incorporate a heavy atom that show anomalous diffraction into the crystals

Question 20

What is the cycle of macro molecular crystallography

Answer 20

Calculate electron density from the data and phases

Fit the model to the electron density

Refine the model using data

Do again until you decide model is good enough

Question 21

What does table 2 describe

Answer 21

The refined model