Introduction to Macromolecular Crystallography E-Book

Alexander McPherson

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 575

Veröffentlichungsjahr: 2011

Beschreibung

A comprehensive and approachable introduction to crystallography -- now updated in a valuable new edition The Second Edition of this well-received book continues to offer the most concise, authoritative, and easy-to-follow introduction to the field of crystallography. Dedicated to providing a complete, basic presentation of the subject that does not assume a background in physics or math, the book's content flows logically from basic principles to methods, such as those for solving phase problems, interpretation of Patterson maps and the difference Fourier method, the fundamental theory of diffraction and the properties of crystals, and applications in determining macromolecular structure. This new edition includes a vast amount of carefully updated materials, as well as two completely new chapters on recording and compiling X-ray data and growing crystals of proteins and other macromolecules. Richly illustrated throughout to clarify difficult concepts, this book takes a non-technical approach to crystallography that is ideal for professionals and graduate students in structural biology, biophysics, biochemistry, and molecular biology who are studying the subject for the first time.

Leseprobe

CONTENTS

PREFACE

CHAPTER 1 AN OVERVIEW OF MACROMOLECULAR CRYSTALLOGRAPHY

WHAT DO WE MEAN BY THE STRUCTURE OF SOMETHING?

AN ANALOGY

A LENS AND OPTICAL DIFFRACTION PATTERNS

HOW X-RAY DIFFRACTION WORKS

THE PHASE PROBLEM

THE ELECTRON DENSITY

CHAPTER 2 CRYSTALLIZATION OF MACROMOLECULES

CRYSTALS GROW FROM SUPERSATURATED SOLUTIONS

WHY CRYSTALS GROW

PROTEINS PRESENT SPECIAL PROBLEMS FOR CRYSTALLOGRAPHERS

PROPERTIES OF MACROMOLECULAR CRYSTALS

CRYSTALLIZATION STRATEGY

SCREENING AND OPTIMIZATION

CREATING THE SUPERSATURATED STATE

PRECIPITATING AGENTS

FACTORS INFLUENCING PROTEIN CRYSTAL GROWTH

SOME USEFUL CONSIDERATIONS

TYPICAL TRIAL ARRAYS

THE IMPORTANCE OF PROTEIN PURITY AND HOMOGENEITY

SOLUBILIZATION

SEEDING

AUTOMATED CRYSTALLIZATION AND ROBOTICS

IMPORTANT PRINCIPLES

CHAPTER 3 THE NATURE OF CRYSTALS: SYMMETRY AND THE UNIT CELL

THE ASYMMETRIC UNIT

THE SPACE GROUP

THE UNIT CELL

THE LATTICE TRANSLATIONS

SYMMETRY AND EQUIVALENT POSITIONS

WHY SO FEW KINDS OF UNIT CELLS

PRIMITIVE AND CENTERED LATTICES

PLANES, MILLER INDEXES, AND CONVOLUTIONS

THE RECIPROCAL LATTICE

CRYSTALS AS WAVES OF ELECTRONS IN THREE-DIMENSIONAL SPACE

CHAPTER 4 WAVES AND THEIR PROPERTIES

THE PROPERTIES OF WAVES

WAVES AS VECTORS AND COMPLEX NUMBERS

ADDITION OF WAVES

MANIPULATING VECTORS

SOME USEFUL WAVE RELATIONSHIPS

THE FOURIER SYNTHESIS, PLANES, AND THE ELECTRON DENSITY

CHAPTER 5 DIFFRACTION FROM POINTS, PLANES, MOLECULES, AND CRYSTALS

DIFFRACTION PATTERN OF AN ARBITRARY ARRAY OF POINTS IN SPACE

DIFFRACTION FROM EQUALLY SPACED POINTS ALONG A LINE

DIFFRACTION FROM A PLANE, FAMILIES OF PLANES, AND LATTICES OF POINTS

CONTINUOUS AND DISCONTINUOUS TRANSFORMS

DIFFRACTION FROM A CRYSTAL

THE STRUCTURE FACTOR FOR A CRYSTAL

THE STRUCTURE FACTOR AS A PRODUCT OF TRANSFORMS

TEMPERATURE FACTORS

CENTERS OF SYMMETRY

FRIEDEL’S LAW

ANOMALOUS DISPERSION EFFECTS

THE ELECTRON DENSITY EQUATION

THE PHASE PROBLEM

CHAPTER 6 INTERPRETATION OF DIFFRACTION PATTERNS

DIFFRACTION PATTERNS, PLANES, AND RECIPROCAL SPACE

EWALD’S SPHERE

CRYSTAL SYMMETRY AND THE SYMMETRY OF THE DIFFRACTION PATTERN

SYMMETRY AND SYSTEMATIC ABSENCES

ANALYSIS OF DIFFRACTION PATTERNS

SYMMETRY IN DIFFRACTION SPACE

MORE THOUGHTS ON SPACE GROUPS

OTHER INFORMATION IN DIFFRACTION PATTERNS

CHAPTER 7 DATA COLLECTION

WHAT IS INVOLVED

X-RAY SOURCES AND THE PRODUCTION OF X RAYS

DETECTORS AND THE RECORDING OF DIFFRACTION INTENSITIES

DATA MANAGEMENT PROCEDURES

CRYSTAL MOUNTING AND HANDLING

X-RAY DATA PROCESSING

SCALING OF X-RAY DIFFRACTION DATA

REAL SPACE AND DIFFRACTION SPACE

CHAPTER 8 SOLVING THE PHASE PROBLEM

PATTERSON METHODS

THE HEAVY ATOM METHOD

THE R FACTOR AND CRYSTALLOGRAPHIC REFINEMENT

ISOMORPHOUS REPLACEMENT

FORMULATION OF ISOMORPHOUS REPLACEMENT IN PROTEIN CRYSTALLOGRAPHY

ISOMORPHOUS REPLACEMENT IN PRACTICE

MOLECULAR REPLACEMENT

PHASE EXTENSION USING NONCRYSTALLOGRAPHIC SYMMETRY

ANOMALOUS SCATTERING APPROACHES

Direct Methods

CHAPTER 9 INTERPRETING PATTERSON MAPS

WHAT IS A PATTERSON MAP

CREATING A PATTERSON MAP FROM A CRYSTAL

PATTERSON MAPS AS MOLECULAR COVOLUTIONS

DECONVOLUTING PATTERSON MAPS

HARKER PLANES OR SECTIONS

USING THE PATTERSON MAP FOR ISOMORPHOUS REPLACEMENT

CHAPTER 10 ELECTRON DENSITY, REFINEMENT, AND DIFFERENCE FOURIER MAPS

RESOLUTION OF ELECTRON DENSITY MAPS

INTERPRETATION OF ELECTRON DENSITY MAPS

CONSTRUCTING A MODEL

MODEL REFINEMENT

RECIPROCAL SPACE REFINEMENT: LEAST SQUARES

REAL SPACE REFINEMENT: DIFFERENCE FOURIER SYNTHESES

ADDITIONAL CONSIDERATIONS IN REFINEMENT

THE FREE R FACTOR

SOME GENERAL OBSERVATIONS

CRITERIA FOR JUDGING A STRUCTURE DETERMINATION

BIOCHEMICAL EXPERIMENTS USING X-RAY CRYSTALLOGRAPHY

THE DIFFERENCE FOURIER METHOD

BIBLIOGRAPHY

INDEX

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Library of Congress Cataloging-in-Publication Data:

McPherson, Alexander, 1944-

Introduction to macromolecular crystallography / Alexander McPherson. – 2e.

p. ; cm.

Includes bibliographical references and index.

ISBN 978-0-470-18590-2 (pbk.)

1. Macromolecules–Structure. 2. X-ray crystallography. I. Title.

[DNLM: 1. Macromolecular Substances. 2. Crystallography, X-Ray. QD

381.9.S87 M478i 2009]

QD381.9.S87M36      2009

548’.83–dc22

2008040417

PREFACE

In 1987 Jim Pflugrath and I initiated a course in practical protein crystallography at Cold Spring Harbor Laboratories. A few years later we were joined by Gary Gilliland and Bill Furey. The four of us have, with unmatched enthusiasm and enjoyment, organized and taught the class until now. It has been an unqualified success by any standard, a source of great pride to each of us, but it began on some uncertain footing.

The first year, Jim and I believed we could simply crack ahead with the practical aspects of the subject, assuming that the students knew the fundamentals of diffraction theory, crystal properties, and the basic concepts of solving the structures of macromolecular crystals. It quickly became apparent to both of us that we were sadly naive.

In an attempt to recover our pedagogical bearings, the author quickly devised a series of lectures, given in spare moments, on the underlying principles of protein crystallography, the bare essential ideas that you have certainly to understand if you intend to apply the crystallographic method in an intelligent manner. That first year, the lectures were delivered in front of a chalkboard by a stone fireplace in the ancient and revered Jones Lab at Cold Spring Harbor. As the course progressed, the lectures moved from Jones Laboratory on the waterfront to Plimpton, and their content evolved over 20 years into the material contained in this book.

The contents of this book are, I believe, the minimum you need to know if you want to practice protein crystallography, and understand why you are doing what you do. It is by no means intended as a comprehensive treatment of the subject. This book is not for professionals or experienced diffractionists. It is meant strictly for students, for scientists outside the field, and particularly for those who, like the author, struggle with mathematics and physics. Only a modest attempt is made to describe the practical aspects of data collection, the intricacies of phasing, nor is crystallographic refinement addressed in the detail it deserves. You will, however, find the principles of diffraction of X-rays by a crystal, how X-ray diffraction can be used to determine macromolecular structures, and the underlying theory by which X-ray crystallography has created a revolution in molecular and structural biology.

This second edition is vastly improved over the first. Numerous small errors present in the original were rooted out and banished, both in the text and the figures. The clarity of numerous figures was improved, and new tables were added and mathematical nomenclature made more uniform. This second edition includes two new chapters, one on macromolecular crystallization, and a second on X-ray diffraction data collection. Refinement and anomalous dispersion phasing are treated somewhat more extensively. More than 35 new figures have been incorporated.

The author was aided immeasurably by the fact that he was himself a miserable physics student, so he deeply sympathizes with those who share his failings in mathematics. This book is written specifically for them, from the perspective of a fellow student who claims no greater intelligence than their own, only more hard-earned experience.

The author wishes to acknowledge and thank three scientists who contributed in more ways than I can describe to this work. It could never have been written without them. They are, of course, Jim Pflugrath, Gary Gilliland, and Bill Furey, my fellow instructors, mentors, colleagues, and friends from the Cold Spring Harbor course. I also wish to thank Debora Felix who helped me organize and collate this material, and Aaron Greenwood who is responsible for many of the illustrations found in the book.

ALEXANDER MCPHERSON