Practical Protein Crystallography

by McRee

Edition: 2nd

ISBN13: 9780124860520

ISBN10: 0124860524

Format: Hardcover

Pub. Date: 1999-09-01

Publisher(s): Elsevier Science

Other versions by this Author

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Summary

Designed for easy use by both beginning and experienced protein crystallographers, the second edition of Practical Protein Crystallography is an essential handbook for any scientist interested in solving a protein structure. The book includes examples of actual experiments and data, electron density maps, and computer methods. This second edition has new material covering CCP4, SHELX, cryocrystallography, MAD and automated fitting. Key Features * In-depth coverage of every aspect of crystallography * Coverage of the small details that can make or break projects * Strongly application-oriented * Exceptionally well illustrated * Simple and easy-to-follow robust methods * Tutorials with actual data available on the Web * Useful for a broad spectrum of scientists

Foreword to the Second Edition

xiii

Preface to the Second Edition

Acknwledgements

xix

Laboratory Techniques

Preparing Protein Samples

(5)

History and Purification

(1)

Exchanging Buffers

(1)

Concentrating Samples

(1)

Storage of Samples

(1)

Ultrapurification

(1)

Protein Crystal Growth

(11)

Protein Solubility Grid Screen

(1)

Initial Trials

(4)

Growth of X-Ray Quality Crystals

(4)

Crystal Storage and Handling

(1)

Crystal Soaking

(2)

Anaerobic Crystals

(3)

Data Collection Techniques

Preparing Crystals for Data Collection

(8)

Crystals-Mounting Supplies

(1)

Mounting Crystals

(5)

Drying Crystals

(1)

Preventing Crystals Slippage

(1)

Optical Alignment

(3)

X-Ray Sources

(5)

Nickel Foil Filtering

(1)

Filtering by Monochromators

(2)

Focusing with Mirrors

(1)

Increasing Brillance with Mirrors

(1)

Preliminary Characterization

(25)

Precession Photography

(4)

Rotation Photography

(6)

Blind Region

(1)

White-Radiation Laue Photography

(2)

Space Group Determination

(7)

Unit-Cell Determination

(1)

Evaluation of Crystal Quality

(3)

Heavy-Atom Derivative Scanning with Film

(3)

Overall Data Collection Strategy

(6)

Unique Data

(2)

Bijvoet Data

(1)

Indexing of Data

(3)

Overview of Older Film Techniques

(1)

Four-Circle Diffractometer Data Collection

(2)

Area Detector Data Collection

(6)

Increasing Signal-to-Noise Ratio

(1)

Image Plate Data Collection

(2)

Synchrotron Radiation Light Sources

(3)

Differences from Standard Sources

(1)

Special Synchrotron Techniques

(1)

Time-Resolved Data Collection

(1)

Data Reduction

(6)

Integration of Intensity

(1)

Error Estimation

(1)

Polarization Correction

(1)

Lorentz Correction

(1)

Decay or Radiation Damage

(1)

Absorption

(3)

Computational Techniques

Terminology

(9)

Reflection

(2)

Resolution

(1)

Coordinate Systems

(2)

R-Factor

(1)

Space Groups and Symmetries

(1)

Matrices for Rotations and Translation

100

(1)

B-Value

100

(1)

Anisotropic B-Values

101

(1)

Basic Computer Techniques

102

(13)

File Systems

102

(1)

Portability Considerations

103

(1)

Setting Up Your Environment

104

(1)

File Formats and mmCIF

104

(7)

CCP4 Crystallographic Programs

111

(4)

Data Reduction and Statistical Analysis

115

(9)

Evaluation of Data

115

(1)

Filtering of Data

116

(1)

Merging and Scaling Data

117

(3)

Heavy-Atom Statistics

120

(4)

The Patterson Synthesis

124

(13)

Patterson Symmetry

125

(1)

Calculating Pattersons

125

(2)

Harker Sections

127

(1)

Solving Heavy-Atom Difference Pattersons

128

(9)

Fourier Techniques

137

(8)

Types of Fourier

137

(8)

Solving Heavy Atoms with Fouriers

145

(1)

Isomorphous Replacement Phasing

145

(17)

Heavy-Atom Refinement

145

(1)

Isomorphous Phasing

146

(7)

Heavy-Atom Phasing Statistics

153

(1)

Including Anomalous Scattering

154

(7)

Fine-Tuning of Derivatives

161

(1)

Molecular Replacement

162

(9)

Rotation Methods

163

(5)

Translation Methods

168

(3)

Noncrystallographic Symmetry

171

(5)

Self-Rotation Function

175

(1)

Density Modification

176

(6)

Solvent Flattering

176

(2)

Histogram Modification

178

(4)

Multiwavelength Data with Anomalous Scattering

182

(11)

Choice of Wavelengths

185

(3)

Collection of Data

188

(1)

Location of Anomalous Scatterers

188

(1)

Phasing of Data

189

(4)

Refinement of Coordinates

193

(24)

Available Software

193

(1)

Rigid-Body Refinement

194

(1)

R-Factor or Correlation Search for Rigid Groups

194

(1)

Protein Refinement

195

(2)

Evaluating Errors

197

(5)

Very-High Resolution Refinement with SHELX-97

202

(11)

Block Diagonal Calculations

213

(2)

SHELX Refinement Strategy

215

(2)

Fitting of Maps

217

(48)

Calculating Electron Density Maps

217

(6)

Evaluating Map Quality

223

(2)

Fitting and Stereochemistry

225

(7)

Chain Tracing

232

(11)

General Fitting

243

(18)

Phase Bias

261

(3)

Adding Waters and Substrates

264

(1)

Analysis of Coordinates

265

(6)

Lattice Packing

265

(1)

Hydrogen Bonding

266

(1)

Solvent-Accessible Surfaces

266

(5)

XtalView Tutorials

Installation

271

(1)

Obtaining Help

272

(1)

XView

272

(31)

XView Widgets

273

(1)

The xtalmgr

274

(3)

Preparing Data

277

(4)

Merging Heavy-Atom Data

281

(1)

Patterson Solutions

282

(2)

Bijvoet Difference Pattersons

284

(1)

Difference Fouriers

284

(1)

Heavy-Atom Refinement and Phase Calculations

285

(4)

Absolute Configuration (Hand)

289

(1)

Enantiomorphic Space Groups

290

(1)

Exporting Data

290

(1)

Xfit

290

(2)

Atom Stack

292

(1)

Fitting with the Mouse

293

(2)

Additional Xfit Functions

295

(2)

Semiautomated Fitting

297

(6)

A Typical Manual Fitting Session with Xfit

303

(23)

Loading the Map

305

(1)

Contouring the Map

305

(2)

Combining Phases

307

(1)

Improving Phases

308

(2)

Saving Phases

310

(1)

Some Additional Xfit Features

310

(2)

Fitting a Residue

312

(7)

Raster 3D

319

(1)

Model Window

320

(2)

SfCalc Window

322

(3)

Finding Geometry Errors

325

(1)

Editing Waters

325

(1)

Interfacing to Other Programs

326

(3)

XPLOR, TNT, PROLSQ, and Other Refinement Programs

328

(1)

Protein Crystallography Cookbook

Multiple Isomorphous Replacement

329

(37)

Patterson from Endonuclease III

331

(3)

Single-Site Patterson from Photoactive Yellow Protein

334

(3)

Two-Site Patterson from Photoactive Yellow Protein

337

(2)

Complete Solution of Chromatium vinosum Cytochrome c'

339

(27)

Mutant Studies

366

(14)

MKT D235E Mutant

370

(1)

SOD C6A Mutant

371

(9)

Substrate--Analog Example

380

(4)

Isocitrate--Aconitase

380

(4)

Molecular Replacement

384

(4)

Yeast Copper--Zinc Superoxide Dismutase

385

(3)

Multiwavelength Anomalous Dispersion (MAD) Phasing

388

(22)

CuA Subunit from T. thermophilus Cytochrome c Oxidase

388

(1)

XAS Scan

389

(1)

Data Collection

389

(3)

Patterson Maps

392

(18)

Cryocrystallography: Basic Theory and Methods

Peter R. David

Overview

410

(1)

Theory

411

(2)

Room Temperature versus Low-Temperature Crystallgraphy

413

(2)

Cryogenic Safety

415

(1)

Equipment

416

(7)

Crystal Supports

418

(2)

Making Loops

420

(3)

Crystal Loop Mounting Techniques

423

(4)

The Use of Platinum Wire

424

(1)

Attaching Pins to Goniometer Heads

425

(2)

Crystal Storage Overview

427

(5)

Lists of Materials

428

(1)

Additional Practical Considerations

429

(1)

Manipulating and Storing Frozen Crystals

429

(1)

Storing Crystals for Later Use

430

(2)

Crystal Removal and Storage

432

(9)

Freezing Away from the Cold Stream

434

(1)

Selecting a Cryoprotectant

435

(1)

Testing Cryprotectant Solutions

435

(1)

Setup

436

(1)

Method

437

(1)

Rationale

438

(2)

Cryoprotectant Optimization

440

(1)

Crystal Handling

441

(4)

Osmotic Effects

441

(4)

APPENDIX A Crystallographic Equations in Computer Code

445

(10)

APPENDIX B Useful Web Sites

455

(8)

Practical Protein Crystallography II Web Sites

455

(1)

Software Web Sites

455

(4)

Databases

459

(1)

Synchrotrons

459

(1)

Useful Information

460

(1)

Heavy-Atom Information

460

(1)

Crystallization

461

(1)

X-Ray Anomalous Scattering

461

(1)

X-Ray Equipment Vendors

461

(1)

Crystallographic Associations

461

(2)

Index

463

Practical Protein Crystallography

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Table of Contents