Crystallographic Methods of Structural Biology
Category
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Abstract
STB 533. Crystallographic Methods of Structural Biology
Course Syllabus and Class Schedule
Fall Semester. Class meetings 10:30-11:45 am Tuesdays and Fridays
The goal of the course is that students acquire sufficient knowledge and understanding of the basic principles of biomolecular crystal structure analysis that they will be able to comfortably, and with interest and insight, read and comprehend the articles in Volume F of the International Tables for Crystallography: Crystallography of Biological Macromolecules, and articles in the current and recent literature reporting research in structural molecular biology by diffraction methods.
Textbooks for the course are:
Eaton E. Lattman and Patrick J. Loll (2008). Protein Crystallography: A Concise Guide. Baltimore, Maryland: Johns Hopkins University Press.
Bernhard Rupp (2010). Biomolecular Crystallography. Principles, Practice, and Applications to Structural Biology. New York: Garland Science, Taylor and Francis Group, LLC. See also http://www.ruppweb.org/ for valuable supplementary materials.
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Dates |
Topics |
Instructor |
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26, 29 Aug. |
Introduction Protein structural elements: 1° aa sequence, 2° α-helix, β strand, β sheet, loop, 3° domain fold, 4° domain assembly; Overview of biomacromolecular crystallography Rupp, chs. 1-4 (Only §§ 1.1-1.5 and 3.2) |
Blessing |
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2, 5 Sept. 9, 12
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Geometrical crystallography Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation and the Ewald construction; Reciprocal space and the reciprocal lattice Rupp, ch. 5 |
Blessing |
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16, 19 Sept. 23, 26
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X-Ray diffraction physics X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6 |
Blessing |
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30 Sept, 3 Oct. 7, 10 |
Statistics and probability in crystallography Descriptive statistics – error propagation; Probability distributions – joint, marginal, and conditional; Likelihood and Bayesian inference Rupp, ch. 7 Mid-term exam |
Blessing |
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14, 17 Oct. 21, (24)
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Diffraction measurements Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2) |
Snell
(Blessing) |
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(28), 31 Oct. 4, (7)
(Fri., 7 Nov. BHT meeting) |
Diffraction measurements (cont’d) Instrumentation – robotic sample handling, pixel detectors; Data collection – local and remote control software; Data processing – data reduction and error analysis Rupp, chs. 8 and 6 (§6.4 and §6.5) |
Snell
(Blessing) |
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11, 14 Nov. 18, 21 |
Structure determination – the phase problem The “fundamental theorem” of structural crystallography; Fourier theory; The Patterson function; Patterson maps, Harker sections; Molecular replacement methods Rupp, chs. 9, 10 |
Blessing |
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25, (28) Nov. 2, 5 Dec.
(Fri., 28 Nov. Thanksgiving recess) |
Structure modeling and refinement SIR, MIR, SAD, SIR/SAD, MAD methods; Stereochemical restraints; NCS averaging and constraints; Fourier methods; Least-squares methods; Maximum likelihood methods; Energy minimization methods Rupp, chs. 11, 12 |
Blessing |
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9, 12 Dec. |
Structure refinement and validation Precision indices; Uncertainty estimates; Ramachandran plots; Richardson MolProbity analysis; Real-space density residual Rupp, ch. 13 |
Blessing |
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16 Dec. |
Final exam |
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Location
Hauptman-Woodward Institute
| Lecture Number/Topic | |||||
|---|---|---|---|---|---|
| Crystallographic Methods - Introduction and Overview | |||||
| Dr. Bob Blessing
Introduction
Protein structural elements: 1° aa sequence, 2° α-helix, β strand, β sheet, loop, 3° domain fold, 4° domain assembly; Overview of … |
|||||
| Crystallographic Methods - Geometrical Crystallography - Part I | |||||
| Dr. Bob Blessing
Geometrical crystallography
Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation … |
|||||
| Crystallographic Methods - Geometrical Crystallography - Part II | |||||
| Dr. Bob Blessing
Geometrical crystallography
Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation … |
|||||
| Crystallographic Methods - X-ray Diffraction Physics - Part I | |||||
| Dr. Bob Blessing
X-Ray diffraction physics
X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal … |
|||||
| Crystallographic Methods - X-ray Diffraction Physics - Part II | |||||
| Dr. Bob Blessing
X-Ray diffraction physics
X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal … |
|||||
| Crystallographic Methods - X-ray Diffraction Physics - Part III | |||||
| Dr. Bob Blessing
X-Ray diffraction physics
X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal … |
|||||
| Crystallographic Methods - X-ray Diffraction Physics - Part IV | |||||
| Dr. Bob Blessing
X-Ray diffraction physics
X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal … |
|||||
| Crystallographic Methods - X-ray Diffraction Physics - Part V | |||||
| Dr. Bob Blessing
X-Ray diffraction physics
X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal … |
|||||
| Crystallographic Methods - X-ray Diffraction Physics - Part VI | |||||
| Dr. Bob Blessing
X-Ray diffraction physics
X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal … |
|||||
| Crystallographic Methods - X-ray Diffraction Physics - Part VII | |||||
| Dr. Bob Blessing
X-Ray diffraction physics
X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal … |
|||||
| Crystallographic Methods - X-ray Diffraction Physics - Part VIII | |||||
| Dr. Bob Blessing
X-Ray diffraction physics
X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal … |
|||||
| Crystallographic Methods - X-ray Diffraction Physics - Part IX | |||||
| Dr. Bob Blessing
X-Ray diffraction physics
X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal … |
|||||
| Crystallographic Methods - Crystallographic Symmetry - Part I | |||||
| Dr. Edward Snell
Diffraction measurements
Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic … |
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| Crystallographic Methods - Crystallographic Symmetry - Part II | |||||
| Dr. Edward Snell
Diffraction measurements
Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic … |
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| Crystallographic Methods - Crystallographic Symmetry - Part III | |||||
| Dr. Edward Snell
Diffraction measurements
Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic … |
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