Protein Structure

Lecture 7 Video 4

๐ŸงŠ Lecture Summary โ€” Reciprocal Lattice, Ewald Sphere & Diffraction Geometry


๐Ÿ” What is the Reciprocal Lattice (Big Idea)

The reciprocal lattice is a mathematical way to describe X-ray diffraction patterns.

  • Each reciprocal lattice point = one diffracted X-ray beam
  • Each beam comes from a set of crystal planes with spacing ( d )
  • These planes are labeled by Miller indices (hkl)

๐Ÿ‘‰ Key construction rule:

  • From the real crystal lattice:
    • Draw planes (like 110, 120, 130โ€ฆ)
    • From the origin draw a vector perpendicular to that plane
    • Length of vector = ( 1/d_ )
    • The endpoint is a reciprocal lattice point with same (hkl)

This means:

Real space planes โ†’ become points in reciprocal space

This is the fundamental mapping used in crystallography.


๐Ÿ“ Relationship Between Miller Indices and Distance

As Miller index increases:

  • Real space plane spacing decreases
  • Therefore:

rac{1}{d} ext{ increases}

So reciprocal lattice vectors become longer.

๐Ÿ’ก Example:

  • 110 โ†’ shorter reciprocal vector
  • 120 โ†’ longer
  • 130 โ†’ even longer

Because planes get closer together.


๐Ÿ“ Reciprocal Axes vs Real Axes

There is a reciprocal relationship between unit cell sizes:

Real unit cellReciprocal unit cell
LargeSmall
SmallLarge

Example insight:

  • Proteins โ†’ very large unit cells
  • Therefore:
    • Reciprocal lattice is dense
    • Diffraction spots on detector are close together

Small molecule crystals:

  • Small unit cell
  • Diffraction spots widely spaced

This is something you actually observe experimentally.


๐Ÿ“ Direction Relationships (Very Important Exam Concept)

Even when angles โ‰  90ยฐ:

  • ( a^* ) is perpendicular to plane BC
  • ( b^* ) is perpendicular to plane AC
  • ( c^* ) is perpendicular to plane AB

So reciprocal axes are always:

Normal vectors to real lattice planes


๐ŸŒ The Ewald Sphere (Geometrical Condition for Diffraction)

Now comes one of the most important visual models in crystallography.

๐ŸŽฏ Concept

  • Incoming X-ray has wavevector length = ( 1/lambda )
  • Draw a sphere with radius ( 1/lambda )
  • Place crystal at center
  • Place reciprocal lattice origin at beam tail

๐Ÿ‘‰ Diffraction happens ONLY when a reciprocal lattice point touches the sphere

Because:

  • This means Braggโ€™s law is satisfied

So:

Reciprocal point on Ewald sphere โ†’ diffraction spot recorded.

This is purely a geometrical representation of Braggโ€™s law.


๐Ÿ”„ Why We Rotate the Crystal

When you rotate the crystal:

  • Real lattice rotates
  • Reciprocal lattice rotates
  • New reciprocal points intersect the Ewald sphere

Therefore:

๐Ÿ‘‰ New reflections appear on detector.

This is how we collect thousands of reflections for structure solution.


๐ŸŽฏ Detector Geometry & Missing Reflections

Not all possible reflections are recorded.

Reasons:

1๏ธโƒฃ Detector size limitation

A reflection may satisfy Braggโ€™s law but:

  • If diffracted beam misses detector โ†’ not recorded

Solution:

  • Move detector closer

2๏ธโƒฃ Resolution sphere (Crystal quality limit)

Crystal disorder limits:

  • Maximum observable reciprocal lattice radius
  • Therefore limits resolution

Outside this sphere:

  • No diffraction (even if geometry allows)

3๏ธโƒฃ Beam stop shadow

Most X-rays are not diffracted.

To protect detector:

  • A beam stop blocks direct beam
  • Creates a shadow region with no data

Very common feature in diffraction images.


๐Ÿ“ธ Precession Photographs (Special Case)

If crystal is perfectly aligned:

  • Diffraction pattern becomes highly symmetric
  • You can directly see:
    • HK plane
    • Axes directions
    • Reflection spacing

From this:

You can calculate reciprocal lattice spacing โ†’ then unit cell dimensions

Because:

A' = rac{A^*}{CF} cdot lambda

This shows:

Unit cell parameters can be determined directly from diffraction geometry.


๐Ÿง  Space Group Determination Logic

In real experiments:

  • Crystal orientation is random
  • We collect many reflections during rotation

Then software:

  1. Builds 3D reciprocal lattice
  2. Tests all possible space groups
  3. Chooses best symmetry fit

Important reasoning:

  • Low symmetry (triclinic) can fit anything
  • But if high symmetry fits โ†’ very likely correct

Because symmetry produces systematic reflection patterns.


โญ Ultra-Short Take-Home Messages

โœ… Reciprocal lattice = diffraction language โœ… Reciprocal vector length = (1/d) โœ… Large protein unit cell โ†’ dense diffraction spots โœ… Diffraction occurs when reciprocal point hits Ewald sphere โœ… Crystal rotation = sampling reflections โœ… Detector geometry + crystal order limit data โœ… Diffraction symmetry โ†’ helps determine space group

Quiz

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