We will be holding a Rigaku School for Practical Crystallography on basic topics in crystallography from January 10-14 and 17-21, 2022 from 0800-0930 CDT. (Use this Time Zone converter to determine your local time.)

The majority of the time will be spent on small molecule crystallography. This is a great opportunity for people interested in crystallography to gain a basic foundation of single crystal analysis from a practical point of view.

We also recognize that some students may not be able to join the live lectures by Zoom. We will make recordings of the lessons available for download shortly after the lectures so that students can keep up with the School and take the exam in the same manner as those who attended the live lectures. However, in order to take the exam and receive a certificate of achievement, you will need to register for the School at the link above.

We hope that you both enjoy and gain something from this School and look forward to meeting you, virtually.

Paul Swepston Joseph Ferrara Fraser White
School Directors: Dr. Paul Swepston, Dr. Joseph Ferrara and Dr. Fraser White

Program

Lecturer: Mathias Meyer

Class description: The scope of this practical school is ‘single-crystal area detector diffractometry’.

Today’s single-crystal diffraction instrumentation is characterized by highly brilliant X-ray sources, precise multi-axes goniometers and fast in case of Rigaku photon counting area detectors.

The critical parameter in experimentation is the required resolution of the diffraction experiment. While in PX experiments the regime is in many cases ‘Connectivity’ experiments (due to the diffraction power of large cell proteins), in the SM crystallography it ranges from ‘Connectivity (Interactive Crystallography)’ to ‘Standard IUCR resolution’ experiments (question of some hrs) and ends with sophisticated ‘High resolution charge density’ experiments (the master class). The introduction will explain this notion of resolution and try to give a ‘price’ for its requirement. The price may mean time, success, processing. The user should be aware what question he/she asks to and from the experiment. We will explain how to plan experiments for these three resolution types.

As life is sometimes is a challenge, more hurdles appear during experimentation like sample twinning, sample mosaicity (from single crystal to powder), ‘tragedies’ of experimenting (sample mount, cooling, fixing artifacts)… Modern software allows dealing with these (at least for the instructed…).

The upcoming set of seminars will explore all these areas further in detail.

Lecturer: Bernhard Spingler

Class description: The lecture will introduce into the field of single crystal growth of small molecules. Basic concepts and methods as well as the latest developments in the scientific literature will be presented.

Lecturer: Pierre Le Maguerès

Class description: Rigaku single crystal X-ray diffractometers all come with CrysAlisᴾʳᵒ, a user-inspired data collection and data processing software for small molecule and protein crystallography. Designed around an easy-to-use graphical user interface, CrysAlisᴾʳᵒ can be operated under fully automatic or manual control, allowing users different levels of intervention according to whether an easy data collection is carried out or a more problematic case must be tackled, such as a twinned crystal, a pseudo-symmetry issue in the lattice or a modulated structure.

We will give an overview of the most commonly used techniques to crystallize small molecules compounds. This will be followed by a live analysis of a well-diffracting small molecule crystal, using the Rigaku microfocus sealed tube X-ray diffractometer, the XtaLAB Synergy-S. We will cover crystal mounting/centering and screening/indexing. Beyond demonstrating the CrysAlisᴾʳᵒ capabilities, tips for the best practice for each of these steps will be discussed.

We will also cover strategy calculation and data collection. We will show how concurrent data processing in CrysAlisᴾʳᵒ and structure solution using AutoChem (an automated version of Olex2) are performed even as data collection proceeds. Lastly, a feature very unique to CrysAlisᴾʳᵒ will be demonstrated: ‘What Is This’. This feature allows for the collection of a fast data set to 1 Å for the purpose of getting the connectivity of a compound, as quality control for what is in the crystal when a detailed and refined crystal structure is not needed.

Lecturer: Christian Schürmann

Class description: CrysAlisPro offers an elaborate integration routine. While the default mode of this routine works great for most cases, sometimes it is beneficial to adjust the integration settings to the special requirements of the data. It is therefore good to have a decent understanding of the computational steps during the integration. This Webinar covers the computational steps during the integration procedure, the user options for these steps, and how these options can be employed for the integration of problematic data.

Lecturer: Christian Göb

Class description: Finalization of data means the preparation of an HKL file, the essence of a single crystal diffraction experiment. CrysAlisPro offers a great automatic routine from indexation to structure solution. The Finalization Dialogue, on the other hand, allows the user to manually edit all parameters in the preparation of HKL files like scaling, absorption correction, error model, space group determination and many other functions. The various given options will be explained, and their influence on the data will be shown by the use of practical examples.

On day five, we will focus on face indexing and absorption correction.

Lecturer: Christian Göb

Class description: Finalization of data means the preparation of an HKL file, the essence of a single crystal diffraction experiment. CrysAlisPro offers a great automatic routine from indexation to structure solution. The Finalization Dialogue, on the other hand, allows the user to manually edit all parameters in the preparation of HKL files like scaling, absorption correction, error model, space group determination and many other functions. The various given options will be explained, and their influence on the data will be shown by the use of practical examples.

On day six, we will discuss the scaling of data, the inspection of data and space group determination.

Lecturer: Horst Puschmann

Class description: We will solve and refine a simple structure using Olex2. We will move on to progressively more tricky cases in this short whirlwind tour of Olex2.

There will be many tips and tricks, and we will cover subjects including modelling of complex disorder, dealing with twinning and even venture into the exciting new waters of anharmonic refinement and the use of non-spherical form factors in the refinement of routine X-ray structures.

Lecturer: Fraser White

Class description: At every step of the crystallographic experiment, from data collection to structure refinement, it is necessary to ensure that certain standards are met to ensure the integrity of the scientific result. While modern software endeavours to provide a high level of guidance and even automation which can help to ensure that the majority of structures have no issues, for various reasons, such as unknown sample characteristics or behaviours, problems can still exist. It is therefore essential for any crystallographer to understand and know how to approach problems with experiments, structures and the files associated with them. Before publication any issues must be identified and rectified or explained to satisfy crystallographic referees and enable an easy path to publication. Fortunately modern crystallographers have access to tools such as CheckCIF which can perform a series of test which identify a wide range of issues from physical inconsistencies, chemical problems or missed information which should be provided as part of the publication process. Additionally our own CrysAlisPro software contains some additional checks which can also assist in the avoidance of publication issues. In this presentation some common issues, their origins and step which might be taken to resolve them are discussed along with software tools and features which may help in such situations.

Lecturer: Jakub Wojciechowski

Class description: This class will provide a brief introduction to the theory of absolute structure determination, but will mostly focus on the practical approach of data collection, refinement, and validation. Selecting an experimental condition and proper data collection strategy is crucial for adequate validation of the absolute structure. The validation is performed by calculation of the specific parameter (Flack, Parson or Hooft), during the crystal structure model refinement.

After this class, you should be able to understand the relation between sample composition and data quality requirements; be ready to correctly chose experimental conditions for diffraction data collection resulting in a valid absolute structure with the help of CrysAlisPro software; perform absolute structure refinement and validation in Shelxl/Olex2 program and extract the information required for publication.

Lecturer: Pierre Le Maguerès

Class description: CrysAlisPro is an excellent program for processing non-merohedral twinned data, thanks to clear and intuitive visualization and manipulation of the intertwined diffraction patterns in the reciprocal space, an excellent indexing algorithm and a powerful procedure for deconvoluting overlapping reflections and assigning the correct intensity to each. Using a simple twinned data set collected on an organic compound, we will demonstrate and explain each one of these steps by performing live data processing and scaling in CrysAlisPro. The last steps of structure refinement in Olex2 for this twinned structure will also be demonstrated.

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