Crystal Structure Refinement A Crystallographer's Guide to SHELXL,9780198570769

Crystal Structure Refinement A Crystallographer's Guide to SHELXL

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Edition: CD
ISBN13: 9780198570769
ISBN10: 0198570767
Format: Hardcover
Pub. Date: 2006-09-07
Publisher(s): Oxford University Press
List Price: $148.35

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Summary

Crystal Structure Refinement is a mixture of textbook and tutorial. As A Crystallographers Guide to SHELXL it covers advanced aspects of practical crystal structure refinement, which have not been much addressed by textbooks so far. After an introduction to SHELXL in the first chapter, a brief survey of crystal structure refinement is provided. Chapters three and higher address the various aspects of structure refinement, from the treatment of hydrogen atoms to the assignment of atom types, to disorder, to non-crystallographic symmetry and twinning. One chapter is dedicated to the refinement of macromolecular structures and two short chapters deal with structure validation (one for small molecule structures and one for macromolecules). In each of the chapters the book gives refinement examples, based on the program SHELXL, describing every problem in detail. It comes with a CD-ROM with all files necessary to reproduce the refinements.

Author Biography


Dr. Peter Muller
Department of Chemistry
Massachusetts Institute of Technology
77 Massachusetts Avenue, Building 2, Room 325
Cambridge, MA 02139, USA
Dr. Regine Herbst-Irmer
Department of Structural Chemistry
Institute of Inorganic Chemistry
University of Gottingen
Tammannstr. 4
D-37077 Gottingen, Germany
Prof. Dr. Anthony L. Spek
Laboratory of Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8
3584 CH Utrecht, The Netherlands
Dr. Thomas R. Schneider
IFOM - The FIRC Institute of Molecular Oncology
Biocrystallography and Structural Bioinformatics
Via Adamello 16
I-20139 Milan, Italy
Dr. Michael R. Sawaya
Research Faculty, UCLA Technology Center
University of California Los Angeles
Box 951662
Los Angeles, CA 90095-1662, USA
Peter Muller has worked in George Sheldrick's research group for over five years, where he received a thorough crystallographic education. He studied chemistry and crystallography (M.S. in 1997) and received his Ph.D. with George Sheldrick in 2001 on a thesis entitled "Problems of Modern High-Resolution Single-Crystal X-Ray Structure Determination" From 2001 to 2004, he spent three years in Los Angeles as a postdoc in David Eisenberg's group at UCLA. There he worked in the field of molecular and structural biology. Currently, he is the director of the X-ray diffraction facility at MIT.
Dr. Muller taught basic and advanced crystallography (both theory and lab classes) in Gottingen, Los Angeles and now at MIT, and has held several structure refinement workshops around the USA and in Germany.
For further details please see also online CV: http://web.mit.edu/x-ray/pmueller/CV.html>

Table of Contents

1 SHELXL
1(6)
Peter Müller
1.1 The SHELX program suite
1(2)
1.1.1 SHELXTL and other programs
1(2)
1.2 SHELXL
3(5)
1.2.1 Program organization
3(1)
1.2.2 The instruction file name.ins
4(1)
1.2.3 The reflection data file name.hkl
5(1)
1.2.4 Merging data in SHELXL
5(1)
1.2.5 The connectivity table
6(1)
2 Crystal structure refinement
7(19)
Peter Müller
2.1 Least-squares refinement
8(1)
2.1.1 Refinement against F or F²—is that a question?
9(1)
2.2 Weak data and high-resolution cut-off
9(2)
2.3 Residual factors
11(1)
2.4 Parameters
12(1)
2.5 Constraints
13(3)
2.5.1 Site occupancy factors
13(1)
2.5.2 Special position constraints
13(1)
2.5.3 Rigid group constraints
14(1)
2.5.4 Floating origin constraints
15(1)
2.5.5 Hydrogen atoms
15(1)
2.5.6 Constraints in SHELXL
15(1)
2.6 Restraints
16(6)
2.6.1 Geometrical restraints
17(2)
2.6.2 Restraints on displacement parameters
19(2)
2.6.3 Other restraints
21(1)
2.7 Free variables in SHELXL
22(1)
2.8 Results
23(2)
2.8.1 Bond lengths and angles
23(1)
2.8.2 Torsion angles
23(1)
2.8.3 Atoms on common planes
24(1)
2.8.4 Hydrogen bonds
24(1)
2.8.5 The RTAB command
24(1)
2.8.6 The MORE command
25(1)
2.8.7 The .cif file
25(1)
2.9 Refinement problems
25(1)
3 Hydrogen atoms
26(16)
Peter Müller
3.1 X—H bond lengths and Ueq values of H atoms
26(1)
3.2 Hydrogen bound to different atom types
27(2)
3.2.1 Hydrogen bound to carbon atoms
27(1)
3.2.2 Hydrogen bound to nitrogen and oxygen
28(1)
3.2.3 Hydrogen bound to metals
29(1)
3.3 Placing hydrogen atoms in SHELXL
29(3)
3.3.1 List of most common m and n values in HFIX commands
30(1)
3.3.2 Semi free refinement of acidic hydrogen atoms
31(1)
3.4 Hydrogen bonds in SHELXL
32(1)
3.5 Examples
32(10)
3.5.1 Routine hydrogen atom placement: C31H54MON2O2
32(3)
3.5.2 Hydrogen atoms in a Zr-hydride
35(2)
3.5.3 Acidic hydrogen atoms and hydrogen bonds
37(5)
4 Atom type assignment
42(14)
Peter Müller
4.1 All electrons are blue
42(1)
4.2 Chemical knowledge
43(1)
4.3 Crystallographic knowledge
43(2)
4.4 Examples
45(12)
4.4.1 Tetrameric InCl3—the N or O question
45(3)
4.4.2 A cobalt salt
48(2)
4.4.3 Unclear central metal atom
50(6)
5 Disorder
56(41)
Peter Müller
5.1 Types of disorder
57(2)
5.1.1 Substitutional disorder
57(1)
5.1.2 Positional disorder
58(1)
5.1.3 Mess—a special case of disorder
59(1)
5.2 Refinement of disorder
59(8)
5.2.1 Refinement of disorder with SHELXL
59(8)
5.3 Examples
67(31)
5.3.1 Gallium-iminosilicate—Disorder of two ethyl groups
68(5)
5.3.2 Disorder of a Ti(III) compound
73(7)
5.3.3 A mixed crystal treated as occupancy disorder
80(1)
5.3.4 Disorder of solvent molecules
81(10)
5.3.5 Three types of disorder in one structure: cycloikositetraphenylene
91(6)
6 Pseudo-Symmetry
97(9)
Peter Müller
6.1 Global pseudo-symmetry
98(1)
6.2 True NCS
98(1)
6.3 Examples
99(7)
6.3.1 Pn or P21/n
99(4)
6.3.2 [Si(NH2)2CH(SiMe3)2]2: P1 with Z = 12
103(3)
7 Twinning
106(44)
Regine Herbst-Irmer
7.1 Definition of a Twin
106(3)
7.2 Classification of twins
109(9)
7.2.1 Twinning by merohedry
109(2)
7.2.2 Twinning by pseudo-merohedry
111(1)
7.2.3 Twinning by reticular merohedry
112(2)
7.2.4 Non-merohedral twins
114(4)
7.3 Tests for twinning
118(1)
7.4 Structure solution
119(1)
7.5 Twin refinement
120(1)
7.6 Determination of the absolute structure
121(1)
7.7 Warning signs of twinning
121(1)
7.8 Examples
122(27)
7.8.1 Twinning by merohedry
122(5)
7.8.2 An example of pseudo-merohedral twinning
127(3)
7.8.3 First example of twinning by reticular merohedry
130(3)
7.8.4 Second example of twinning by reticular merohedry
133(7)
7.8.5 First example of non-merohedral twinning
140(4)
7.8.6 Second example of non-merohedral twinning
144(5)
7.9 Conclusions
149(1)
8 Artefacts
150(9)
Peter Müller
8.1 What is an Artefact?
150(4)
8.1.1 Libration
151(1)
8.1.2 Shortened triple bonds
152(1)
8.1.3 Hydrogen positions
153(1)
8.1.4 Fourier truncation errors
153(1)
8.2 What is not an artefact?
154(1)
8.3 Example
154(6)
8.3.1 Fourier termination error in C3OH47N9Zr5
154(5)
9 Structure validation
159(7)
Anthony L. Spek
9.1 Validation
160(1)
9.2 Validation tests implemented in PLATON
161(3)
9.2.1 Missed symmetry
161(1)
9.2.2 Voids
161(1)
9.2.3 Displacement ellipsoids
162(1)
9.2.4 Bond lengths and angles
162(1)
9.2.5 Atom type assignment
162(1)
9.2.6 Intermolecular contacts
163(1)
9.2.7 Hydrogen bonds
163(1)
9.2.8 Connectivity
163(1)
9.2.9 Disorder
163(1)
9.2.10 Reflection data
164(1)
9.2.11 Refinement parameters
164(1)
9.3 When to validate
164(1)
9.4 Concluding remarks
164(2)
10 Protein refinement 166(21)
Thomas R. Schneider
10.1 Atomic resolution refinement vs. standard refinement
168(3)
10.1.1 Anisotropic displacement parameters
168(1)
10.1.2 Multiple discrete sites
169(1)
10.1.3 Hydrogens
169(1)
10.1.4 Solvent
170(1)
10.1.5 Standard uncertainties
170(1)
10.2 Stages of a typical refinement
171(13)
10.2.1 Getting started
171(1)
10.2.2 Rough adjustments of the model at 1.5 Å
172(1)
10.2.3 Including data to atomic resolution
173(1)
10.2.4 Going anisotropic
174(1)
10.2.5 Rebuilding the model at atomic resolution
174(4)
10.2.6 Inclusion of hydrogens—when and how
178(1)
10.2.7 Solvent
179(1)
10.2.8 Finalizing the model
180(2)
10.2.9 Estimation of coordinate uncertainties
182(1)
10.2.10 Analysis and presentation of the structure
183(1)
10.3 Examples
184(4)
10.3.1 Course of a typical refinement of a protein
184(1)
10.3.2 Determination of standard uncertainties for protein-ligand contacts
185(2)
11 Protein structure (cross) validation 187(10)
Michael R. Sawaya
11.1 PROCHECK
188(3)
11.2 WHAT_CHECK
191(2)
11.2.1 List of close non-bonded contacts
191(1)
11.2.2 Unsatisfied hydrogen bond donors/acceptors
192(1)
11.2.3 List of isolated water molecules
193(1)
11.3 Verify3D
193(1)
11.4 Errat
194(1)
11.5 Prove
195(2)
12 General remarks 197(7)
Peter Müller
12.1 How many refinement cycles do I need?
197(1)
12.2 What to do with NPD atoms?
197(1)
12.3 How many restraints may I use in a structure?
198(1)
12.4 Coordination geometries of some cations
199(2)
12.5 Some typical bond lengths
201(1)
12.6 Resolution tables
202(2)
References 204(5)
Further Reading 209(2)
Index 211

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