November 09

1
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

2
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 theoryMathematical 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

3

• Time Tue. and Thu. 200 330 PM
• Place Donner Laboratory (Rm 208)
• Text "Outline of Crystallography for
  Biologists"
• By David Blow (Oxford Univ. Press, 2003)
• Lecturers
• Sung-Hou Kim
• (SHKim_at_cchem.berkeley.edu 486-4333)
• Paul Adams
• (PDAdams_at_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

4
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

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Imaging of an object by lens Light can be bent
and focused by lens
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Optical Microscopy
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X-Ray Diffraction No X-ray lens
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Dimensional Scaling

• Biological macromolecules
• Size of atoms 1 ? (0.1 nm)
• Need radiation of 0.1 nm wavelength, l
• He-Ne laser has l632.8 nm 0.6238 mm
• Need objects made of atoms of 0.6 mm
  (6000X) or greater

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Demonstration

• He-Ne laser (l632.8 nm) vs. X-ray (l0.1 nm)
• masks vs. atoms

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Objects and Diffraction patterns (MolecularTran
sform)
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Sampling of Molecular transform By Multiple
copies of an object
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Reciprocal Relationship Size and Separation
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Diffraction of Gases and Liquids
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Conservation of Symmetry and Orientation
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Demonstration

• One long thin slit
• ( One long thin molecule)
• One long thick slit
• ( One long fat molecule)
• Aligned multiple slits
• ( Parallel aligned long molecules)

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Diffraction from One Slit
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Diffraction from Many Slits
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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

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Diffraction from a slit (a long molecule)
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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)

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Diffraction Amplitude from One or Two Slits
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Diffraction from Two Slits
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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

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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