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Book Details
Abstract
Protein crystallography has become vital to further understanding the structure and function of many complex biological systems. In recent years, structure determination has progressed tremendously however the quality of crystals and data sets can prevent the best results from being obtained. With contributions from world leading researchers whose software are used worldwide, this book provides a coherent approach on how to handle difficult crystallographic data and how to assess its quality. The chapters will cover all key aspects of protein crystallography, from instrumentation and data processing through to model building. This book also addresses challenges that protein crystallographers will face such as dealing with data from microcrystals and multi protein complexes. This book is ideal for both academics and researchers in industry looking for a comprehensive guide to protein crystallography.
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Cover | Cover | ||
| FOREWORD Protein Crystallography: Faster, Smaller, Stronger | v | ||
| Contents | xi | ||
| Chapter 1 Practical Approaches for In Situ X-ray Crystallography: from High-throughput Screening to Serial Data Collection | 1 | ||
| 1.1 Introduction | 1 | ||
| 1.1.1 What Exactly Is In Situ? | 1 | ||
| 1.1.2 Goals of In Situ Experiments | 3 | ||
| 1.1.3 Challenges of In Situ Methods | 4 | ||
| 1.1.4 Enabling Technologies | 5 | ||
| 1.2 In Situ Screening at the Synchrotron: Standard SBS Plates | 7 | ||
| 1.2.1 Development History | 7 | ||
| 1.2.2 Plate Handling Hardware | 9 | ||
| 1.2.3 Plate Optimization for In Situ | 9 | ||
| 1.2.4 Automation and Pipeline Integration | 10 | ||
| 1.3 Further Developments: Scale Reduction and Microfluidics | 11 | ||
| 1.3.1 Small Formats | 11 | ||
| 1.3.2 Microfluidic Methods for In Situ | 13 | ||
| 1.4 The Emergence of Serial In Situ Data Collection | 15 | ||
| 1.4.1 Thin-film Sandwiches | 15 | ||
| 1.4.2 Liquid Manipulation Methods | 19 | ||
| 1.5 Conclusion and Outlook | 20 | ||
| Acknowledgements | 20 | ||
| References | 21 | ||
| Chapter 2 Delivery of GPCR Crystals for Serial Femtosecond Crystallography | 28 | ||
| 2.1 Introduction | 28 | ||
| 2.2 Process Overview | 30 | ||
| 2.3 Achieving Major Milestones | 31 | ||
| 2.3.1 Large-scale Production of Stable Receptor Constructs | 31 | ||
| 2.3.2 Crystallization of Receptor Constructs | 38 | ||
| 2.3.3 SFX Data Collection | 39 | ||
| 2.4 Summary of Successful GPCR Structural Studies at XFELs | 42 | ||
| Acknowledgements | 46 | ||
| References | 46 | ||
| Chapter 3 The Mesh&Collect Pipeline for the Collection of Multi-crystal Data Sets in Macromolecular Crystallography | 54 | ||
| 3.1 Introduction | 54 | ||
| 3.2 Dozor | 59 | ||
| 3.3 Hierarchical Cluster Analysis (HCA) | 59 | ||
| 3.4 Mesh&Collect in Practice | 60 | ||
| 3.4.1 Solving the Crystal Structures of Membrane Proteins with Very Small Crystals | 61 | ||
| 3.4.2 Multi-crystal Data Collection for Ligand Binding Studies | 63 | ||
| 3.4.3 De novo Structure Solution using Mesh&Collect | 64 | ||
| 3.4.4 Mesh&Collect for the I-SAD/I-SIRAS Solutions of the Crystal Structure of the KR Light-Driven Sodium Pump | 68 | ||
| 3.4.5 Mesh&Collect at Room Temperature | 69 | ||
| 3.5 The Pitfalls of HCA | 69 | ||
| 3.6 ccCluster | 75 | ||
| 3.7 Merging of Partial Data Sets Using Genetic Algorithms | 75 | ||
| 3.7.1 Grouping Partial Data Sets into Chromosomes | 77 | ||
| 3.7.2 Fitness Evaluation | 77 | ||
| 3.7.3 GA Optimisation | 79 | ||
| 3.7.4 Case Study: LUX | 79 | ||
| 3.8 MeshBest | 80 | ||
| 3.8.1 NarQ Crystals Analysed by a Mesh Scan | 82 | ||
| 3.8.2 A 'Mishmash' of Thaumatin Crystals | 82 | ||
| 3.9 Conclusions | 83 | ||
| References | 84 | ||
| Chapter 4 Radiation Damage in Macromolecular Crystallography | 88 | ||
| 4.1 Introduction | 88 | ||
| 4.2 How Do X-ray Photons Interact with Matter? | 90 | ||
| 4.3 Global and Specific Radiation Damage Effects at 100 K and Below | 92 | ||
| 4.4 Estimating the Absorbed Dose and Dose Limits | 96 | ||
| 4.5 X-ray Induced Changes in Chromophore-containing Proteins at 100 K | 102 | ||
| 4.6 Global and Specific Radiation Damage Above 100 K and at Room Temperature | 102 | ||
| 4.7 Recruitment of Radiation-induced Changes to Study Macromolecular Function | 103 | ||
| 4.8 Radiation-damage Induced Phasing | 104 | ||
| 4.9 Does Radiation Damage Depend on Dose Rate and/or on the Incident Beam Energy at 100 K? | 105 | ||
| 4.10 How Can Radiation Damage Be Minimised? | 106 | ||
| 4.11 Radiation Damage in Serial Femtosecond Crystallography at XFELs | 108 | ||
| Acknowledgements | 109 | ||
| References | 109 | ||
| Chapter 5 Data Quality Analysis | 117 | ||
| 5.1 Introduction | 117 | ||
| 5.2 Accuracy versus Precision and Merged versus Unmerged Data | 118 | ||
| 5.3 Sources of Error | 119 | ||
| 5.3.1 Random Error | 120 | ||
| 5.3.2 Systematic Error | 121 | ||
| 5.3.3 Outliers | 123 | ||
| 5.3.4 Radiation Damage | 124 | ||
| 5.4 Estimating Errors | 125 | ||
| 5.4.1 Estimation of σ(Ihkl) | 125 | ||
| 5.4.2 ISa, an Indicator for Systematic Error | 126 | ||
| 5.4.3 Rmerge, Rsym and Rmeas – Indicators for Unmerged Data | 126 | ||
| 5.4.4 Rmrgd-I, Rp.i.m., Ranom and CC1/2 – Indicators for Merged Data | 127 | ||
| 5.4.5 Rd, Rcum and B Factor – Indicators for Radiation Damage | 129 | ||
| 5.4.6 Data Completeness | 130 | ||
| 5.5 Use of Metrics | 130 | ||
| 5.5.1 BLEND and Merging Multiple Crystals and/or Data Sets | 130 | ||
| 5.5.2 Identifying Rogue Data Sets and Linking Data and Model Quality | 131 | ||
| 5.5.3 Determination of a High-resolution Cut-off | 132 | ||
| 5.5.4 Things to Consider When Collecting and Analysing Data | 134 | ||
| 5.6 Concluding Remarks | 137 | ||
| References | 138 | ||
| Chapter 6 Structure Determination at Low-resolution, Anisotropic Data and Crystal Twinning | 140 | ||
| 6.1 Introduction | 140 | ||
| 6.2 Experimental | 141 | ||
| 6.2.1 Protein Expression and Purification | 141 | ||
| 6.2.2 Protein Crystallization and Derivatization | 142 | ||
| 6.2.3 X-ray Diffraction Data Collection and Analysis | 142 | ||
| 6.3 Results and Discussion | 142 | ||
| 6.3.1 Data Collection and Radiation Damage | 142 | ||
| 6.3.2 Data Reduction and Anisotropy | 143 | ||
| 6.3.3 Twinning Detection and Analysis | 144 | ||
| 6.3.4 Molecular Replacement and Structure Solution | 147 | ||
| 6.3.5 Difference Fourier Analysis | 149 | ||
| 6.3.6 Attempts in Experimental Phasing | 151 | ||
| 6.3.7 Comparison of the NorM-NG Structures | 152 | ||
| 6.3.8 Ligand-binding Site | 153 | ||
| 6.4 Conclusion | 154 | ||
| Acknowledgements | 155 | ||
| References | 155 | ||
| Chapter 7 Structure Determination and Refinement of Large Macromolecular Assemblies at Low Resolution | 157 | ||
| 7.1 Introduction | 157 | ||
| 7.2 Crystallization, Data Collection and Processing | 159 | ||
| 7.3 Crystal Characterisation | 161 | ||
| 7.4 CSN4 | 165 | ||
| 7.5 Heavy-atom-soaked Derivative Crystals | 165 | ||
| 7.6 Initial Phasing | 166 | ||
| 7.7 Subunit Identification and Selenomethionine Phasing | 169 | ||
| 7.8 Initial Model Building | 170 | ||
| 7.9 Model Completion | 171 | ||
| 7.10 Analysis of CSN Conformational Dynamics Aided by a P1 Crystal Form | 174 | ||
| 7.11 Conclusions | 177 | ||
| Acknowledgements | 178 | ||
| References | 178 | ||
| Chapter 8 Crystallography with X-ray Free Electron Lasers | 181 | ||
| 8.1 X-ray Free Electron Lasers – An Introduction | 181 | ||
| 8.2 Radiation Damage at XFELs | 184 | ||
| 8.3 Serial Femtosecond Crystallography | 185 | ||
| 8.3.1 SFX Experimental Setup | 185 | ||
| 8.3.2 SFX Early Achievements | 187 | ||
| 8.3.3 SFX Sample Delivery and Data Collection Rates | 189 | ||
| 8.4 Time-resolved Serial Femtosecond Crystallography | 192 | ||
| 8.4.1 Pump Probe Serial Femtosecond Crystallography | 193 | ||
| 8.4.2 Mix-and-inject Serial Femtosecond Crystallography | 194 | ||
| 8.5 Serial Femtosecond Crystallography Data Analysis | 194 | ||
| 8.5.1 SFX Data Collection Overview | 194 | ||
| 8.5.2 Data Collection Monitoring | 195 | ||
| 8.5.3 Hit Finding | 195 | ||
| 8.5.4 Bragg Diffraction Analysis: Indexing, Merging, Post-refinement | 197 | ||
| 8.5.5 Phasing and Model Refinement | 202 | ||
| 8.5.6 De novo Phasing of SFX Data | 203 | ||
| 8.5.7 SFX Data Volumes and Data Sharing | 205 | ||
| 8.6 New Developments | 206 | ||
| 8.6.1 Sparse Crystal Pattern Indexing | 206 | ||
| 8.6.2 Nanocrystal Shape Transform Phasing | 206 | ||
| 8.6.3 Continuous Diffuse Scattering | 206 | ||
| 8.6.4 Single-layer 2D Crystals | 207 | ||
| 8.6.5 Incoherent Diffractive Imaging | 208 | ||
| 8.7 Conclusion | 208 | ||
| Acknowledgements | 209 | ||
| References | 209 | ||
| Subject Index | 225 |