Crystal Structure Refinement A

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.

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>

1 SHELXL

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Peter Müller

1.1 The SHELX program suite

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1.1.1 SHELXTL and other programs

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1.2 SHELXL

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1.2.1 Program organization

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1.2.2 The instruction file name.ins

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1.2.3 The reflection data file name.hkl

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1.2.4 Merging data in SHELXL

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1.2.5 The connectivity table

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2 Crystal structure refinement

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Peter Müller

2.1 Least-squares refinement

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2.1.1 Refinement against F or F²—is that a question?

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2.2 Weak data and high-resolution cut-off

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2.3 Residual factors

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2.4 Parameters

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2.5 Constraints

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2.5.1 Site occupancy factors

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2.5.2 Special position constraints

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2.5.3 Rigid group constraints

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2.5.4 Floating origin constraints

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2.5.5 Hydrogen atoms

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2.5.6 Constraints in SHELXL

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2.6 Restraints

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2.6.1 Geometrical restraints

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2.6.2 Restraints on displacement parameters

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2.6.3 Other restraints

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2.7 Free variables in SHELXL

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2.8 Results

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2.8.1 Bond lengths and angles

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2.8.2 Torsion angles

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2.8.3 Atoms on common planes

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2.8.4 Hydrogen bonds

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2.8.5 The RTAB command

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2.8.6 The MORE command

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2.8.7 The .cif file

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2.9 Refinement problems

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3 Hydrogen atoms

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Peter Müller

3.1 X—H bond lengths and Ueq values of H atoms

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3.2 Hydrogen bound to different atom types

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3.2.1 Hydrogen bound to carbon atoms

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3.2.2 Hydrogen bound to nitrogen and oxygen

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3.2.3 Hydrogen bound to metals

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3.3 Placing hydrogen atoms in SHELXL

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3.3.1 List of most common m and n values in HFIX commands

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3.3.2 Semi free refinement of acidic hydrogen atoms

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3.4 Hydrogen bonds in SHELXL

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3.5 Examples

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3.5.1 Routine hydrogen atom placement: C31H54MON2O2

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3.5.2 Hydrogen atoms in a Zr-hydride

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3.5.3 Acidic hydrogen atoms and hydrogen bonds

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4 Atom type assignment

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Peter Müller

4.1 All electrons are blue

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4.2 Chemical knowledge

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4.3 Crystallographic knowledge

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4.4 Examples

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4.4.1 Tetrameric InCl3—the N or O question

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4.4.2 A cobalt salt

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4.4.3 Unclear central metal atom

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5 Disorder

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Peter Müller

5.1 Types of disorder

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5.1.1 Substitutional disorder

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5.1.2 Positional disorder

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5.1.3 Mess—a special case of disorder

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5.2 Refinement of disorder

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5.2.1 Refinement of disorder with SHELXL

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5.3 Examples

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5.3.1 Gallium-iminosilicate—Disorder of two ethyl groups

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5.3.2 Disorder of a Ti(III) compound

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5.3.3 A mixed crystal treated as occupancy disorder

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5.3.4 Disorder of solvent molecules

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5.3.5 Three types of disorder in one structure: cycloikositetraphenylene

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6 Pseudo-Symmetry

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Peter Müller

6.1 Global pseudo-symmetry

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6.2 True NCS

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6.3 Examples

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6.3.1 Pn or P21/n

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6.3.2 [Si(NH2)2CH(SiMe3)2]2: P1 with Z = 12

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7 Twinning

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Regine Herbst-Irmer

7.1 Definition of a Twin

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7.2 Classification of twins

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7.2.1 Twinning by merohedry

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7.2.2 Twinning by pseudo-merohedry

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7.2.3 Twinning by reticular merohedry

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7.2.4 Non-merohedral twins

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7.3 Tests for twinning

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7.4 Structure solution

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7.5 Twin refinement

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7.6 Determination of the absolute structure

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7.7 Warning signs of twinning

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7.8 Examples

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7.8.1 Twinning by merohedry

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7.8.2 An example of pseudo-merohedral twinning

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7.8.3 First example of twinning by reticular merohedry

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7.8.4 Second example of twinning by reticular merohedry

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7.8.5 First example of non-merohedral twinning

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7.8.6 Second example of non-merohedral twinning

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7.9 Conclusions

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8 Artefacts

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Peter Müller

8.1 What is an Artefact?

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8.1.1 Libration

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8.1.2 Shortened triple bonds

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8.1.3 Hydrogen positions

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8.1.4 Fourier truncation errors

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8.2 What is not an artefact?

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8.3 Example

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8.3.1 Fourier termination error in C3OH47N9Zr5

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9 Structure validation

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Anthony L. Spek

9.1 Validation

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9.2 Validation tests implemented in PLATON

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9.2.1 Missed symmetry

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9.2.2 Voids

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9.2.3 Displacement ellipsoids

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9.2.4 Bond lengths and angles

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9.2.5 Atom type assignment

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9.2.6 Intermolecular contacts

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9.2.7 Hydrogen bonds

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9.2.8 Connectivity

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9.2.9 Disorder

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9.2.10 Reflection data

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9.2.11 Refinement parameters

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9.3 When to validate

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9.4 Concluding remarks

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10 Protein refinement

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Thomas R. Schneider

10.1 Atomic resolution refinement vs. standard refinement

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10.1.1 Anisotropic displacement parameters

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10.1.2 Multiple discrete sites

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10.1.3 Hydrogens

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10.1.4 Solvent

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10.1.5 Standard uncertainties

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10.2 Stages of a typical refinement

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10.2.1 Getting started

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10.2.2 Rough adjustments of the model at 1.5 Å

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10.2.3 Including data to atomic resolution

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10.2.4 Going anisotropic

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10.2.5 Rebuilding the model at atomic resolution

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10.2.6 Inclusion of hydrogens—when and how

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10.2.7 Solvent

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10.2.8 Finalizing the model

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10.2.9 Estimation of coordinate uncertainties

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10.2.10 Analysis and presentation of the structure

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10.3 Examples

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10.3.1 Course of a typical refinement of a protein

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10.3.2 Determination of standard uncertainties for protein-ligand contacts

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11 Protein structure (cross) validation

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Michael R. Sawaya

11.1 PROCHECK

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11.2 WHAT_CHECK

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11.2.1 List of close non-bonded contacts

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11.2.2 Unsatisfied hydrogen bond donors/acceptors

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11.2.3 List of isolated water molecules

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11.3 Verify3D

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11.4 Errat

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11.5 Prove

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12 General remarks

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Peter Müller

12.1 How many refinement cycles do I need?

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12.2 What to do with NPD atoms?

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12.3 How many restraints may I use in a structure?

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12.4 Coordination geometries of some cations

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12.5 Some typical bond lengths

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12.6 Resolution tables

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References

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Crystal Structure Refinement A Crystallographer's Guide to SHELXL

Summary

Author Biography

Table of Contents

Supplemental Materials