Real-time monitoring of large-scale crystal growth using batch crystallization for serial crystallography

Article Multidisciplinary Sciences

Beef tallow injection matrix for serial crystallography

Ki Hyun Nam

Summary: Serial crystallography allows the visualization of dynamic processes in macromolecular structures at room temperature, and beef tallow is introduced as a stable and controllable sample delivery medium in SX experiments.

SCIENTIFIC REPORTS (2022)

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Article Crystallography

Processing of Multicrystal Diffraction Patterns in Macromolecular Crystallography Using Serial Crystallography Programs

Ki Hyun Nam

Summary: Cryocrystallography is a widely used method for determining the crystal structure of macromolecules. This study introduces a method for processing multicrystal diffraction data using a serial crystallography program, which allows for the integration of diffraction patterns from multiple crystals in a single image.

CRYSTALS (2022)

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Article Biochemical Research Methods

Crystal structure of the domain-swapped dimeric maltodextrin-binding protein MalE from Salmonella enterica

Lulu Wang et al.

Summary: The crystal structure of a domain-swapped dimeric MalE from Salmonella enterica (named SeMalE) in complex with maltopentaose is reported for the first time, showing a distinct structure from typical monomeric MalE family members. These findings provide new insights into maltodextrin-binding MalE proteins.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2022)

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Article Biochemistry & Molecular Biology

Hit and Indexing Rate in Serial Crystallography: Incomparable Statistics

Ki Hyun Nam

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

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Article Crystallography

Pink-Beam Serial Synchrotron Crystallography at Pohang Light Source II

Yongsam Kim et al.

Summary: In this study, a pink-beam serial synchrotron crystallographic experiment was conducted at the 1C beamline at the Pohang Light Source II, successfully determining lysozyme crystal structures at a high resolution of 1.7 angstrom. Different X-ray exposure positions and times were compared to analyze their impact on data collection and structure determination.

CRYSTALS (2022)

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Article Chemistry, Multidisciplinary

Combination of an inject-and-transfer system for serial femtosecond crystallography

Keondo Lee et al.

Summary: Serial femtosecond crystallography (SFX) is a method that enables the determination of macromolecular crystal structures at room temperature with minimal radiation damage and provides time-resolved molecular dynamics. A combined inject-and-transfer system (BITS) method for sample delivery in SFX experiments has been introduced, allowing reliable deposition of solution samples on UV ozone-treated polyimide films. This method has been successfully applied to determine the room-temperature structure of lysozyme.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2022)

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Article Chemistry, Multidisciplinary

Upgraded Combined Inject-and-Transfer System for Serial Femtosecond Crystallography

Keondo Lee et al.

Summary: This study introduces an upgraded inject-and-transfer system that improves beamtime efficiency for serial femtosecond crystallography. It is reported that the widely used viscous solution for protein crystallization can be stably deposited on a hydrophobic surface without any special treatment. Additionally, the development of an inject-and-diffuse method for time-resolved studies with liquid applications in the system is presented.

APPLIED SCIENCES-BASEL (2022)

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Article Biochemistry & Molecular Biology

Structural analysis of metal chelation of the metalloproteinase thermolysin by 1,10-phenanthroline

Ki Hyun Nam

Summary: The study aimed to understand the structural basis of zinc metalloproteinase inhibition by 1,10-phenanthroline through X-ray crystallography, revealing interactions between 1,10-phenanthroline and amino acids, as well as metal ions, in the proteinase.

JOURNAL OF INORGANIC BIOCHEMISTRY (2021)

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Article Biochemistry & Molecular Biology

Room-Temperature Structure of Xylitol-Bound Glucose Isomerase by Serial Crystallography: Xylitol Binding in the M1 Site Induces Release of Metal Bound in the M2 Site

Ki Hyun Nam

Summary: The study reveals that xylitol binding to GI causes a change in the geometric coordination of metal binding sites, leading to the rearrangement of metal-binding residues at the M1 and M2 sites. This sheds light on the reason for the decreased metal-binding affinity and enhances understanding of the xylitol-bound state of SruGI for potential industrial applications.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Editorial Material Biochemistry & Molecular Biology

Molecular Dynamics-From Small Molecules to Macromolecules

Ki Hyun Nam

Summary: Studying the structure and dynamics of molecules is crucial for understanding their functions, and can provide valuable insights for various industries such as materials development and drug discovery.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Multidisciplinary Sciences

Polyimide mesh-based sample holder with irregular crystal mounting holes for fixed-target serial crystallography

Ki Hyun Nam et al.

Summary: Serial crystallography (SX) enables determination of macromolecule structure at room temperature with minimal radiation damage and visualization of molecular dynamics. The use of a polyimide mesh-based sample holder with irregularly shaped holes can increase random crystal orientation on the sample holder, leading to expanded applications in FT-SX experiments.

SCIENTIFIC REPORTS (2021)

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Article Biochemical Research Methods

Versatile microporous polymer-based supports for serial macromolecular crystallography

Isabelle Martiel et al.

Summary: Serial data collection using thin supports made of polymer-based membranes has proven to be a useful method for challenging targets with small crystal sizes, weak diffraction, and stringent dose limits. These supports are suitable for a wide range of protein crystals suspended in liquid, including membrane proteins growing in the sponge phase. The sample-deposition method is simple and robust, resulting in optimally thin specimens with low background and minute amounts of mother liquor around the crystals, making it a flexible and adaptable solution for various cases. Thanks to their affordable fabrication, these supports have the potential to become an attractive option for serial experiments at synchrotrons and free-electron lasers.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2021)

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Article Biochemical Research Methods

Crystal structure of human brain-type fatty acid-binding protein FABP7 complexed with palmitic acid

Ki Hyun Nam

Summary: The fatty acid-binding protein FABP7 plays a crucial role in cellular functions and disease processes. When bound to FABP7, palmitic acid exhibits a unique U-shaped conformation, distinct from unsaturated fatty acids. Structural comparisons reveal that the binding of palmitic acid to FABP7 differs from other human FABPs, suggesting a specific interaction pattern.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2021)

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Article Chemistry, Multidisciplinary

Stable sample delivery in a viscous medium via a polyimide-based single-channel microfluidic chip for serial crystallography

Ki Hyun Nam et al.

Summary: Serial crystallography (SX) allows for room-temperature crystal structures with minimal radiation damage and molecular dynamics comprehension. A stable system for sample delivery in a viscous medium via a polyimide-based single-channel microfluidic (PSM) chip was developed, successfully determining room-temperature lysozyme crystal structures at 1.85 angstrom resolution. Ultimately, this method greatly facilitates sample delivery for SX experiments using synchrotron X-rays.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2021)

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Article Instruments & Instrumentation

BL-11C Micro-MX: a high-flux microfocus macromolecular-crystallography beamline for micrometre-sized protein crystals at Pohang Light Source II

Do Heon Gu et al.

Summary: BL-11C is a new protein crystallography beamline located at the Pohang Accelerator Laboratory, made available to users in June 2017. It offers energy tunability in the range of 5.0-20 keV for conventional experiments with a wide range of heavy metals.

JOURNAL OF SYNCHROTRON RADIATION (2021)

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Review Biochemistry & Molecular Biology

Protein X-ray Crystallography and Drug Discovery

Laurent Maveyraud et al.

MOLECULES (2020)

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Article Multidisciplinary Sciences

Shortening injection matrix for serial crystallography

Ki Hyun Nam

SCIENTIFIC REPORTS (2020)

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Article Biochemistry & Molecular Biology

Polysaccharide-Based Injection Matrix for Serial Crystallography

Ki Hyun Nam

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

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Article Chemistry, Multidisciplinary

Stable sample delivery in viscous media via a capillary for serial crystallography

Ki Hyun Nam

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2020)

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Article Chemistry, Multidisciplinary

Application of a high-throughout microcrystal delivery system to serial femtosecond crystallography

Donghyeon Lee et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2020)

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Article Biochemistry & Molecular Biology

Lard Injection Matrix for Serial Crystallography

Ki Hyun Nam

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

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Review Biochemistry & Molecular Biology

Sample Delivery Media for Serial Crystallography

Ki Hyun Nam

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

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Article Biochemical Research Methods

Processing serial crystallography data with CrystFEL: a step-by-step guide

Thomas A. White

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2019)

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Article Multidisciplinary Sciences

Nylon mesh-based sample holder for fixed-target serial femtosecond crystallography

Donghyeon Lee et al.

SCIENTIFIC REPORTS (2019)

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Article Biochemical Research Methods

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Dorothee Liebschner et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2019)

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Article Instruments & Instrumentation

Sample delivery using viscous media, a syringe andasyringe pump for serial crystallography

Suk-Youl Park et al.

JOURNAL OF SYNCHROTRON RADIATION (2019)

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Article Multidisciplinary Sciences

Polyacrylamide injection matrix for serial femtosecond crystallography

Jaehyun Park et al.

SCIENTIFIC REPORTS (2019)

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Article Biochemistry & Molecular Biology

MolProbity: More and better reference data for improved all-atom structure validation

Christopher J. Williams et al.

PROTEIN SCIENCE (2018)

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Article Crystallography

Study on the influence of lysozyme crystallization conditions on crystal properties in crystallizers of varied sizes when temperature is the manipulated variable

Xi H. Tang et al.

JOURNAL OF CRYSTAL GROWTH (2018)

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Review Biochemistry & Molecular Biology

A Bright Future for Serial Femtosecond Crystallography with XFELs

Linda C. Johansson et al.

TRENDS IN BIOCHEMICAL SCIENCES (2017)

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Editorial Material Chemistry, Multidisciplinary

Serial crystallography at synchrotrons and X-ray lasers

Jorg Standfuss et al.

IUCRJ (2017)

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Article Chemistry, Multidisciplinary

Protein crystallography and drug discovery: recollections of knowledge exchange between academia and industry

Tom L. Blundell

IUCRJ (2017)

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Article Biochemistry & Molecular Biology

Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography

Christian G. Roessler et al.

STRUCTURE (2016)

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Article Multidisciplinary Sciences

Protein crystal screening and characterization for serial femtosecond nanocrystallography

Connie Darmanin et al.

SCIENTIFIC REPORTS (2016)

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Review Biochemistry & Molecular Biology

Structural analysis of enzymes used for bioindustry and bioremediation

Masaru Tanokura et al.

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY (2015)

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Article Allergy

100 Years later: Celebrating the contributions of x-ray crystallography to allergy and clinical immunology

Anna Pomes et al.

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY (2015)

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Article Biochemical Research Methods

Grease matrix as a versatile carrier of proteins for serial crystallography

Michihiro Sugahara et al.

NATURE METHODS (2015)

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Review Crystallography

Protein crystallography from the perspective of technology developments

Xiao-Dong Su et al.

CRYSTALLOGRAPHY REVIEWS (2015)

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Article Chemistry, Physical

Approaches to time-resolved diffraction using an XFEL

John C. H. Spence

FARADAY DISCUSSIONS (2014)

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Review Biochemistry & Molecular Biology

A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits

Mariusz Jaskolski et al.

FEBS JOURNAL (2014)

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Article Biology

Microcrystallization techniques for serial femtosecond crystallography using photosystem II from Thermosynechococcus elongatus as a model system

Christopher Kupitz et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2014)

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Article Biology

Diffraction before destruction

Henry N. Chapman et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2014)

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Article Multidisciplinary Sciences

Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography

Uwe Weierstall et al.

NATURE COMMUNICATIONS (2014)

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Article Biochemical Research Methods

Introduction to protein crystallization

Alexander McPherson et al.

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS (2014)

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Article Biochemical Research Methods

Optimization of crystallization conditions for biological macromolecules

Alexander McPherson et al.

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS (2014)

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Article Chemistry, Multidisciplinary

Room-temperature macromolecular serial crystallography using synchrotron radiation

Francesco Stellato et al.

IUCRJ (2014)

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Article Chemistry, Multidisciplinary

Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data

Anton Barty et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2014)

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Article Biochemical Research Methods

Crystallographic data processing for free-electron laser sources

Thomas A. White et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2013)

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Article Multidisciplinary Sciences

High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

Sebastien Boutet et al.

SCIENCE (2012)

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Article Multidisciplinary Sciences

Femtosecond X-ray protein nanocrystallography

Henry N. Chapman et al.

NATURE (2011)

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Article Biochemical Research Methods

Molecular replacement with MOLREP

Alexei Vagin et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

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Article Optics

Femtosecond protein nanocrystallography-data analysis methods

Richard A. Kirian et al.

OPTICS EXPRESS (2010)

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Article Crystallography

The Factors during Protein Crystallization: A Review

X. X. Li et al.

CRYSTALLOGRAPHY REPORTS (2008)

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Article Physics, Applied

Gas dynamic virtual nozzle for generation of microscopic droplet streams

D. P. DePonte et al.

JOURNAL OF PHYSICS D-APPLIED PHYSICS (2008)

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Article Biochemical Research Methods

Protein crystallization: from purified protein to diffraction-quality crystal

Naomi E. Chayen et al.

NATURE METHODS (2008)

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Article Biochemical Research Methods

Coot:: model-building tools for molecular graphics

P Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2004)

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Review Pathology

x Ray crystallography

MS Smyth et al.

JOURNAL OF CLINICAL PATHOLOGY-MOLECULAR PATHOLOGY (2000)

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Real-time monitoring of large-scale crystal growth using batch crystallization for serial crystallography

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