# Presentation: 662819

## Chem 272 Module A/B (Spring, 2008)

- Macromolecular Crystallography— One of the most powerful method to obtain 3-D structures of biological macromolecules and complexes (others: NMR, Cryo EM)
- Method---Not  intuitively easy to understand, but many steps in the method can be automated by experts
- Users--- The method is robust enough and automated enough, so that the majority of users are going to be non-crystallographers, i.e., biophysicists, biochemists, molecular biologists, cell biologists, etc.
- Warning!! ---3-D structure is very addictive

## Topics

**Introduction of diffraction phenomena **
**Demo: Diffraction from 1D and 2D repeats of simple objects **
**Demo: Diffraction from complex objects: “Convolution” **
**Demo: Diffraction from 3D repeat---e.g. helical objects **
**"Reciprocal lattice" **
**“****Ewald sphere”**
**Diffraction theory—Mathematical approach **
**Diffraction theory---Physical approach**
**Experimentals---X-ray sources, crystallization, etc.  **
**Data Collection and Processing **
**Substructure Determination **
**Experimental Phasing **
**Phasing by Molecular Replacement **
**Phase Improvement **
**Map Interpretation and Model Building **
**Structure Refinement  **
**Twinning **
**Automation****	****	**

## Time:  Tue. and Thu.  2:00 – 3:30 PM
Place:  Donner Laboratory (Rm 208)
Text:  "Outline of Crystallography for Biologists" 
			By David Blow (Oxford Univ. Press, 2003)
Lecturers:  	
		Sung-Hou Kim 
			(SHKim@cchem.berkeley.edu; 486-4333)
		Paul Adams 
			(PDAdams@LBL.gov; 486-4225)

Exam: A brief research proposal (5 pages) by 5/22 
		1. Title and abstract
		2. Background and significance of questions asked
		3. Research plan and feasibility
		4. Possible outcome and interpretation

**Place:  Donner Laboratory (Rm 208)**
**Text:  "Outline of Crystallography for Biologists" **
**	****	****	****By David Blow (Oxford Univ. Press, 2003)**
**Lecturers:  ****	**
**	****	****Sung-Hou Kim **
**	****	****	****(SHKim@cchem.berkeley.edu; 486-4333)**
**	****	****Paul Adams **
**	****	****	****(PDAdams@LBL.gov; 486-4225)**
**Exam: A brief research proposal (5 pages) by 5/22**** **
**	****	****1. Title and abstract**
**	****	****2. Background and significance of questions asked**
**	****	****3. Research plan and feasibility**
**	****	****4. Possible outcome and interpretation**

## Lecture 1

**Introduction of diffraction phenomena**
**	****	****Dimension of objects and the minimum ****	****wavelength of radiation needed to observe the ****	****objects**
**Imaging of an object**
**	****	****Optical microscopy vs. Diffraction**
**Demonstration of diffraction of an object by laser**
**	****	****Relationship between object space and ****	****diffraction space**
**	****	**

## Slide 5

## Imaging of an object by lens:

**Imaging of an object by lens:**
**Light can be bent and focused by lens**

## Optical Microscopy

**Optical Microscopy**

## X-Ray Diffraction:

**X-Ray Diffraction:**
**No X-ray lens**

## Dimensional Scaling

**Biological macromolecules:**
**	****  ****Size of atoms= ~ 1 ****Ǻ****  ****(0.1 nm) **
**	****  ****Need radiation of ~ 0.1 nm wavelength, ******
**He-Ne laser has ********=632.8 nm= 0.6238 ********m**
**	****  ****Need objects made of “atoms” of ~0.6 ****	********m (~6000X) or greater **
**      **

## Demonstration

**He-Ne laser (********=632.8 nm) vs. X-ray (********~0.1 nm)**
**“****masks” vs. atoms**

## Objects 

**Objects **
**and **
**Diffraction patterns**
**(“MolecularTransform”)**

## Sampling of

**Sampling of**
**“****Molecular transform”**
**By**
**Multiple copies**
**of an object**

## “Reciprocal Relationship”: Size and Separation

**“****Reciprocal Relationship”: Size and Separation**

## Diffraction of

- Gases and Liquids

## Conservation of 

**Conservation of **
**Symmetry **
**and **
**Orientation**

## Slide 17

## Demonstration

**One long thin slit **
**	****	****( One long thin “molecule”)**
**One long thick slit **
**	****	****( One long fat “molecule”)**
**Aligned multiple slits**
**	****	****( Parallel aligned long “molecules”)**

## Diffraction from One Slit

**Diffraction from One Slit**

## Diffraction from Many Slits

**Diffraction from Many Slits**

## Fourier Transform

**Amplitude and phase of diffracted wave can be described by mathematical operation of Fourier transform**
**Diffraction intensity is proportional to the square of diffraction amplidude **

## Diffraction from a slit’

**Diffraction from a slit’**
**(a long “molecule”)**

## Slide 23

## Slide 24

## Slide 25

## Demonstration

**Two long thin slit **
**	****	****( One long thin “molecule”)**
**Two long thick slit **
**	****	****( One long fat “molecule”)**
**Aligned multiple two slits**
**	****	****( Parallel aligned long dimer ****	****“molecules”)**

## Diffraction Amplitude from One or Two Slits

**Diffraction Amplitude from One or Two Slits**

## Diffraction from Two Slits

**Diffraction from Two Slits**

## Slide 29

## Demonstration

**Diffraction from a single helical molecule**
**Diffraction from multiple helical molecules aligned in 1-D along helical axis**
**“****Intuitive” interpretation of diffraction pattern of helical molecules**

## Slide 31

## Slide 32

## Summary.  

**Object size and the minimum wave length of radiation to observe it**
**Microscopy and diffraction**
**Monochromatic radiation and diffraction**
**Object and diffraction pattern, “Molecular transform”**
**Conservation of symmetry and orientation**
**Reciprocal relationship of separation**
**Each point of diffraction pattern comes from whole object**
**Molecular transform and sampling**