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Proteins > Xray Crystallography > Flashcards

Xray Crystallography Flashcards

1
Q

When did Bragg invent crystallography?

A

1913 to study NaCl

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2
Q

How many drugs have been designed using crystallography?

A

2

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3
Q

What is the wavelength of an Xray?

A

1A

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4
Q

How long is an angstrom?

A

10^-10m

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5
Q

What characteristics does a wave have?

A

Amplitude
Phase
Length
Frequency

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6
Q

How can crystals be grown?

A

Sandwich/sitting/hanging drop

Vapour diffusion into concentrated reservoir solution

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7
Q

How long does it take to grow a crystal?

A

2 days

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8
Q

How do Xrays interact with crystals?

A

Electrons vibrate when they absorb energy

Aligned electrons send out strong secondary radiation

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9
Q

What type of scattering is produced?

A

Constructive and destructive interference as Bragg’s law

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10
Q

What can be determined from scattering of aligned molecules?

A

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

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11
Q

What information must be known for a fourier transform?

A

amplitudes and phases

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12
Q

Are initial crystals perfect?

A

No-they need to be optimised

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13
Q

What is the structure of a crystal?

A

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

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14
Q

How many types of unit cell are there?

A

4

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15
Q

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

A

14

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16
Q

How many types of assymetric units are there?

A

7

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17
Q

Are crystals fixed structures?

A

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

18
Q

Why are diffraction patterns produced?

A

No lens can focus X rays

19
Q

What does a diffraction pattern look like?

A

Spots of different intensities in resolution shells

20
Q

Where is resolution highest on a diffraction pattern?

A

Outside

21
Q

For what molecules can phase be directly detected?

A

Less than 100 atoms

22
Q

Why is phase needed?

A

For the electron density equation

23
Q

How can phase be detected for large atoms?

A

Multiple Isomorphous replacement
Multiwavelength anomalous dispersion
Molecular replacement

24
Q

Which method of detecting phase is most common?

A

Molecular replacement

25
Q

How does MIR work?

A

> 2 heavy atom soaks change pattern and overlap determines phase

26
Q

What are the disadvantages of MIR?

A

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

27
Q

How does MAD work?

A

Adds selenium ion to produce scattering and fluorescence

28
Q

How does MR work?

A

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

29
Q

What is the main disadvantage of MR?

A

Model bias

30
Q

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

A

Intensities and phases

31
Q

What resolution is needed to fit an electron density map?

A

2A

32
Q

What do electron density maps show?

A

Crystal average of all conformations,
ligands,
water,
ions

33
Q

What do electron density maps not show?

A

Hydrogens
Dynamic regions
Protonation states

34
Q

How are electron density maps improved?

A

By refinement in a semi automated cycle

model-phase-map

35
Q

What is the R factor?

A

The residual factor showing disagreement between observed and computed intensities

36
Q

What R factor value is good for protein?

A

0.2

37
Q

What R factor value is good for organics?

A

0.05

38
Q

What is R free?

A

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

39
Q

What does model validation check?

A 
Atoms are "happy":
Hydrophobicity,
hydrogen bonds
Geometry/Ramachandran plot
No overlaps
40
Q

Why are some old structures in the PDB wrong?

A

Hard to assign small ligands

No Rfree

41
Q

Why is EM an alternative?

A

Shows individual atoms

42
Q

When is NMR used instead?

A

For dynamic molecules that cannot be crystallised

Proteins (12 decks)

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