Day 7/8 part 2

Protein structure

🌊 First: normal X-ray scattering (no anomalous effect)

When X-rays hit atoms in a crystal:

  • Electrons oscillate
  • They re-emit X-rays → scattering

This scattering creates the diffraction pattern.

Normally we assume:

Scattering is purely elastic → no energy is absorbed.

Mathematically:

F_ = F_{-h-k-l}

This means:

  • Friedel pairs have identical intensity

So:

👉 No extra information about phase can be obtained.


⚡ What is anomalous scattering (intuitive idea)

Anomalous scattering happens when:

The atom absorbs some of the X-ray energy and then re-emits it with a small phase shift.

So scattering is no longer perfectly elastic.

This only happens strongly for heavy atoms and only at specific X-ray energies.


🧠 Think of it like this

Normal atom:

  • behaves like a simple mirror → reflects light cleanly

Anomalous atom:

  • behaves like a mirror + sponge
  • it absorbs some energy
  • re-emits with delay and changed amplitude

This “delay” = phase change

That tiny change is what crystallographers exploit.


📊 Mathematical view (simplified)

Normal scattering factor:

f

With anomalous scattering:

f = f_0 + f' + if''

Where:

  • ( f_0 ) → normal scattering
  • ( f' ) → real correction (dispersion)
  • ( f'' ) → imaginary correction (absorption-related)

These extra terms:

👉 change reflection intensities 👉 break Friedel’s law.


🎯 Why is this useful?

Because now:

I(hkl) eq I(-h-k-l)

This intensity difference allows us to:

  • locate heavy atoms
  • estimate phases
  • solve structure.

This is the basis of SAD/MAD phasing.


🔥 What is the absorption edge?

Now the REALLY key idea.

Atoms have core electrons:

  • K-shell
  • L-shell
  • etc.

Each shell has a specific binding energy.


Absorption edge = threshold energy

If X-ray energy becomes high enough to:

eject a core electron

Then absorption suddenly increases.

This sharp increase in absorption vs energy is called:

Absorption edge

It looks like a step in an absorption spectrum.


Why is anomalous scattering strongest there?

At the absorption edge:

  • Atom strongly interacts with X-rays
  • Electron excitation becomes very efficient
  • ( f' ) and ( f'' ) change rapidly

This produces:

  • maximum anomalous signal
  • biggest intensity differences.

So crystallographers:

👉 tune synchrotron wavelength exactly to that edge.


📡 Example (from your lecture)

They used tungsten.

Procedure:

  1. Measure absorption spectrum
  2. Find edge position
  3. Collect diffraction data at:
  • Peak wavelength
  • Inflection wavelength
  • Remote wavelength

This is MAD phasing.


🧠 Super important intuition

Normal diffraction:

  • all atoms scatter similarly
  • symmetry preserved
  • no phase info.

Anomalous diffraction:

  • heavy atoms scatter “weirdly”
  • symmetry slightly broken
  • tiny intensity differences appear
  • these differences encode phase information.

⭐ VERY short exam definition

Anomalous scattering: Deviation from normal elastic X-ray scattering that occurs near an atom’s absorption edge, causing changes in scattering amplitude and phase, which lead to intensity differences between Friedel pairs and allow phase determination.

Absorption edge: The X-ray energy at which core electrons of an atom can be excited or ejected, causing a sharp increase in absorption and strong anomalous scattering effects.

Quiz

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