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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.

 

Dates

Topics

Instructor

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

2, 5 Sept.

9, 12

 

 

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

16, 19 Sept.

23, 26

 

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

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

14, 17 Oct.

21, (24)

 

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)

(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)

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

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

9, 12 Dec.

Structure refinement and validation

    Precision indices; Uncertainty estimates; Ramachandran plots; Richardson MolProbity analysis; Real-space density residual

Rupp, ch. 13

Blessing

16 Dec.

Final exam

 

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 …

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 …

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 …