Xray Crystallography

Question 1

When did Bragg invent crystallography?

Answer 1

1913 to study NaCl

Question 2

How many drugs have been designed using crystallography?

Answer 2

2

Question 3

What is the wavelength of an Xray?

Answer 3

1A

Question 4

How long is an angstrom?

Answer 4

10^-10m

Question 5

What characteristics does a wave have?

Answer 5

Amplitude
Phase
Length
Frequency

Question 6

How can crystals be grown?

Answer 6

Sandwich/sitting/hanging drop

Vapour diffusion into concentrated reservoir solution

Question 7

How long does it take to grow a crystal?

Answer 7

2 days

Question 8

How do Xrays interact with crystals?

Answer 8

Electrons vibrate when they absorb energy

Aligned electrons send out strong secondary radiation

Question 9

What type of scattering is produced?

Answer 9

Constructive and destructive interference as Bragg’s law

Question 10

What can be determined from scattering of aligned molecules?

Answer 10

Distance and number of electrons from diffraction spot pattern interpreted into electron density map by fourier transforms

Question 11

What information must be known for a fourier transform?

Answer 11

amplitudes and phases

Question 12

Are initial crystals perfect?

Answer 12

No-they need to be optimised

Question 13

What is the structure of a crystal?

Answer 13

Assymetric units arranged into a unit cell as the most basic volume

Question 14

How many types of unit cell are there?

Answer 14

4

Question 15

How many types of lattice of repeating unit cells are there?

Answer 15

14

Question 16

How many types of assymetric units are there?

Answer 16

7

Question 17

Are crystals fixed structures?

Answer 17

No, they have enzymatic activity and 50% solvent content in pores

Question 18

Why are diffraction patterns produced?

Answer 18

No lens can focus X rays

Question 19

What does a diffraction pattern look like?

Answer 19

Spots of different intensities in resolution shells

Question 20

Where is resolution highest on a diffraction pattern?

Answer 20

Outside

Question 21

For what molecules can phase be directly detected?

Answer 21

Less than 100 atoms

Question 22

Why is phase needed?

Answer 22

For the electron density equation

Question 23

How can phase be detected for large atoms?

Answer 23

Multiple Isomorphous replacement
Multiwavelength anomalous dispersion
Molecular replacement

Question 24

Which method of detecting phase is most common?

Answer 24

Molecular replacement

Question 25

How does MIR work?

Answer 25

>2 heavy atom soaks change pattern and overlap determines phase

Question 26

What are the disadvantages of MIR?

Answer 26

Soaking can destroy crystal change unit cell dimension poor binding of heavy atom

Question 27

How does MAD work?

Answer 27

Adds selenium ion to produce scattering and fluorescence

Question 28

How does MR work?

Answer 28

Using phases of "model" with sequence >25% identity in same rotation and translation unit cell dimensions in silico

Question 29

What is the main disadvantage of MR?

Answer 29

Model bias

Question 30

What are the 2 pieces of information that contribute to an electron density map?

Answer 30

Intensities and phases

Question 31

What resolution is needed to fit an electron density map?

Answer 31

2A

Question 32

What do electron density maps show?

Answer 32

Crystal average of all conformations, ligands, water, ions

Question 33

What do electron density maps not show?

Answer 33

Hydrogens Dynamic regions Protonation states

Question 34

How are electron density maps improved?

Answer 34

By refinement in a semi automated cycle | model-phase-map

Question 35

What is the R factor?

Answer 35

The residual factor showing disagreement between observed and computed intensities

Question 36

What R factor value is good for protein?

Answer 36

0.2

Question 37

What R factor value is good for organics?

Answer 37

0.05

Question 38

What is R free?

Answer 38

R factor calculated from a 10% subset of values not included in the original refinement

Question 39

What does model validation check?

Answer 39

``` Atoms are "happy": Hydrophobicity, hydrogen bonds Geometry/Ramachandran plot No overlaps ```

Question 40

Why are some old structures in the PDB wrong?

Answer 40

Hard to assign small ligands | No Rfree

Question 41

Why is EM an alternative?

Answer 41

Shows individual atoms

Question 42

When is NMR used instead?

Answer 42

For dynamic molecules that cannot be crystallised