Single Crystal X-ray Diffraction (SC-XRD)

Asia SC-XRD User Meeting 2021 Scientific Program

11-12 November, 09:30 - 6:00 PM IST / 12:00 - 8:30 PM SGT / 15:00 - 11:30 PM AEDT

Day 1

Last update: 25 Oct 2021

Prof. Geoff Jameson (Massey University) - Adventures in protein crystallography with PROTEUM3

We have collected useful data to ~2.6 Å on a small needle crystal of the T109L mutant of a bacterial pectin methyl esterase that challenges processivity by this non-canonical molecular motor. We also have collected data to ~2.4 Å on a thin plate of the DNA mutator protein APOBEC3A, as its inactive E72A mutant, to which substrate DNA oligonucleotide is bound, to reveal in unprecedented detail the nature of the enzyme-DNA interaction. Data have subsequently been collected to better than 2.0 Å on the microfocus MX2 beamline of the Australian Synchrotron for both species.


Dr. Saumen Datta (IICB Kolkata) - An analysis on Ketopantoate reductases, vitamin B5 biosynthesis pathway enzymes from Pseudomonas aeruginosa

Ketopantoate reductases (KPRs) catalyse NADPH-dependent reduction of ketopantoate to pantoate, the rate-limiting step of pantothenate biosynthetic pathway. It is one of the four enzymes involved in pantothenate biosynthesis in bacteria. This pathway is highly important for new antimicrobial lead development as well as from industrial perspective. In this talk a few recent developments on KPRs will be highlighted based on X-ray diffraction data collected on Bruker PHOTON III pixel detector at 100K using Bruker D8 VENTURE diffractometer (home source) and harvested, indexed, integrated and scaled using Proteum3 software suite.


Dr. Rajesh Gonnade (NCL Pune) - Crystal Structure Solution and Refinement of Some Problematic Structures

Although crystal structure solution and refinement have reached the level that even a non-crystallographer can determine the crystal structure and publish it in the journal. This is all because of the automation and reliability of the auto-structures derived from the X-ray intensity data. However, some structures need manual to intervene and expert crystallographers to solve the complex structures. Here, I will discuss the refinement of the highly disordered structures using the APEX3 package.


Prof. Deepak Chopra (IISER Bhopal) - Probing the role of Structure in Function

Recent developments in technology have enabled rapid data acquisition, of both high quality and precision This allows for the determination of structures of compounds that exhibit different properties. In particular, optical, electrical, mechanical and catalytic properties are of interest. The talk shall highlight the relevance of high quality data in unravelling the subtle structural features which substantially contribute to the observed property.


Dr. Ryosuke Miyake (Ochanomizu University) - X-ray structural analysis of giant assembled structures with a short flexible unit: challenge with TXS, rotating anode systems.

We recently succeeded in forming giant cyclic complexes possessing cavities with a diameter of ca. 2 nm using a flexible tripeptide, controlled by metal coordination and hydrogen bonds. We will discuss their structures, including the research stories on single crystal X-ray structural analysis using TXS, rotating anode systems.






Day 2

Prof. Dr. Prabu Sankar Ganesan (Indian Institute of Technology Hyderabad) - Legacy of SCXRD to Infer Agostic and Hydrogen Bonding Interactions

A rare intramolecular Au···H–C(sp3) hydrogen-bonding interaction and luminescent properties of a gold(I) carbene complex will be discussed.  The single-crystal X-ray diffraction analysis of single crystals evidenced the solid-state structure of the mononuclear gold carbene complex, which exhibited the expected linear coordination geometry. The n-heptane arm of the carbene ligand modulates the hydrogen-bonding interaction between Au(I) and the hydrogen atom of one of the CH2 moieties. The packing of the gold(I) carbene complex shows an interesting one-dimensional column in the solid-state due to intermolecular Cl···H interactions.


Dr. Samuel Morris  (NTU Facility for Analysis, Characterisation, Testing and Simulation) - Understanding Piezoelectricity in Layered Single Crystals – a CIPS example. 

We have recently unearthed the atomistic mechanism behind the largest known negative piezoelectric ferroelectric material. This lecture will describe what happens a voltage makes this CIPS crystal massively shrink, compared to almost all known other materials that expand. I will also discuss more recent findings on how halide substitutions can control bond lengths that are integral to the switching capability behind some ferroelectrics.


Prof. Mao Minoura (Rikkyo University) - APEX3 for data analysis at Spring-8

In this presentation, we will focus on how to deal with nonnative-SFRM format frames by Bruker APEX3. These non-SFRM format frames came from the DECTRIS detectors at SPring-8, a synchrotron radiation facility in Japan. Although we were aware of importable formats such as CBF and TIFF, the file conversion was very time-consuming. We also desired to use a reliable integration software, namely SAINT/APEX3. Therefore, we decided to develop a file conversion software that can quickly convert DECTRIS-EIGER/PILATUS frames to the native SFRM format so that we can check the molecular structure during the measurement with APEX3. Here, we would like to introduce the converter "Henkankun-R" using synchrotron radiation images at SPring-8 as an example.