Screen LibraryCrystallography made crystal clear : a guide for users of macromolecular models /
Saved in:
| Main Authors: | |
|---|---|
| Published: |
|
| Literature type: | Book |
| Language: | English |
| Edition: | 3rd ed. |
| Series: |
Complementary science series
|
| Subjects: | |
| Carrier Form: | xxv, 306 p. : ill. (some col.) ; 23 cm. |
| Bibliography: | Includes bibliographical references and index. |
| ISBN: |
9780125870733 (alk. paper) : 0125870736 (alk. paper) |
| Index Number: | QP519 |
| CLC: | O7-62 |
| Call Number: | O7-62/R476/3rd ed. |
| Contents: |
1. Model and molecule -- 2. An overview of protein crystallography -- Thumbnail sketch of protein crystallography -- Introduction -- Crystals -- Nature of crystals -- Growing crystals -- Collecting x-ray data -- Diffraction -- Arrays of simple objects : real and reciprocal lattices -- Intensities of reflections -- Arrays of complex objects -- Three-dimensional arrays -- Coordinate systems in crystallography -- Mathematics of crystallography -- Wave equations : periodic functions -- Complicated periodic functions : Fourier series and sums -- Structure factors : wave descriptions and x-ray reflections -- Electron-density maps -- Electron density from structure factors -- Electron density from measured reflections -- 3. Protein crystals -- Size, structural integrity, and mosaicity -- Multiple crystalline forms -- Water content -- Evidence that solution and crystal structures are similar -- Growing protein crystals -- Growing derivative crystals -- Finding optimal conditions for crystal growth -- Judging crystal quality -- Mounting crystals for data collection -- 4. Collecting diffraction data -- Geometric principles of diffraction -- Generalized unit cell -- Indices of the atomic planes in a crystal -- Conditions that produce diffraction : Bragg's law -- The reciprocal lattice -- Bragg's law in reciprocal space -- Number of measurable reflections -- Unit-cell dimensions -- Unit-cell symmetry -- Collecting x-ray diffraction data -- X-ray sources -- Detectors -- Cameras -- Scaling and postrefinement of intensity data -- Determining unit-cell dimensions -- Symmetry and the strategy of collecting data -- 5. From diffraction data to electron density -- Fourier sums and the Fourier transform -- One-dimensional waves -- Three-dimensional waves -- Fourier mathematics and diffraction -- Structure factor as a Fourier sum -- Electron density as a Fourier sum -- Computing electron density from data -- The phase problem -- Meaning of the Fourier equations -- 6. Obtaining phases -- Two-dimensional representation of structure factors -- Complex numbers in two dimensions -- Structure factors as complex vectors -- Electron density as a function of intensities and phases -- Isomorphous replacement -- Heavy atoms -- Anomalous scattering -- Multiwavelength anomalous diffraction phasing -- Anomalous scattering and the hand problem -- Direct phasing : application of methods from small-molecule crystallography -- Molecular replacement : related proteins as phasing models -- Isomorphous phasing models -- Nonisomorphous phasing models -- Separate searches for orientation and location -- Iterative improvement of phases -- 7. Obtaining and judging the molecular model -- Iterative improvement of maps and models -- First maps -- The model becomes molecular -- Minimizing bias from the model -- Map fitting -- Structure refinement -- Least-square models -- Crystallographic refinement by least squares -- Additional refinement parameters -- Local minima and radius of convergence -- Molecular energy and motion in refinement -- Bayesian methods : ensembles of models -- Convergence to a final model -- Sharing the model -- 8. A user's guide to crystallographic models -- Judging the quality and usefulness of the refined model -- Structural parameters -- Resolution and precision of atomic positions -- Vibration and disorder -- Other limitations of crystallographic models -- Reading a crystallography paper -- 9. Other diffraction methods -- Fiber diffraction -- Diffraction by amorphous materials (scattering) -- Neutron diffraction -- Electron diffraction and cryo-electron microscopy -- Laue diffraction and time-resolved crystallography - 10. Other kinds of macromolecular models -- NMR models -- Assigning resonances -- Determining conformation -- PDB files of NMR models -- Homology models -- Databases of homology models -- 11. Tools for studying macromolecules -- Computer models of molecules -- Two-dimensional images from coordinates -- Into three dimensions : basic modeling operations -- Three-dimensional display and perception -- Types of graphical models -- Touring a molecular modeling program -- Importing and exporting coordinate files -- Loading and saving models -- Viewing models -- Editing and labeling the display -- Coloring - Measuring -- Exploring structural change -- Exploring the molecular surface -- Exploring intermolecular interactions : multiple models -- Displaying crystal packing -- Building models from scratch -- Scripts and macros -- Tools structure analysis and validation -- Tools for modeling protein action -- Appendix : viewing stereo images. |