Hit and Indexing Rate in Serial Crystallography: Incomparable Statistics

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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Editorial Material Crystallography

Serial X-ray Crystallography

Ki Hyun Nam

Summary: Serial crystallography (SX) is an emerging technique to determine macromolecules at room temperature. It provides time-resolved dynamics of target molecules through pump-probe experiments. SX has rapidly developed as a technique for studying room-temperature structures and molecular dynamics of biomolecules. The development of sample delivery techniques and data processing programs is accelerating SX research.

CRYSTALS (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 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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Review Crystallography

Protein Dynamics and Time Resolved Protein Crystallography at Synchrotron Radiation Sources: Past, Present and Future

Jose M. Martin-Garcia

Summary: The ultrabright and ultrashort pulses from XFELs have enabled studies of crystallized molecular machines under 'native' conditions at room temperature. Upgraded synchrotrons with sophisticated focusing optics and fast detectors offer new possibilities for time-resolved crystallography experiments. Increasing publications report new findings in structural dynamics of protein macromolecules using this approach.

CRYSTALS (2021)

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Article Biochemistry & Molecular Biology

Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

Serdar Durdagi et al.

Summary: The text discusses the impact of the COVID-19 pandemic and research efforts to identify effective therapies. Determining the apo structures of SARS-CoV-2 main protease and conducting molecular simulations of known inhibitors provides insights for drug repurposing and design strategies against COVID-19.

STRUCTURE (2021)

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Article Multidisciplinary Sciences

An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography

Agata Butryn et al.

Summary: Serial femtosecond crystallography has provided new opportunities for studying protein dynamics with high resolution. However, the challenge lies in studying enzyme-catalyzed reactions. A drop-on-drop sample delivery system has been proposed in this study, showing potential for widespread application in studying enzyme reactions in crystallography.

NATURE COMMUNICATIONS (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 Chemistry, Multidisciplinary

A reference-based multi-lattice indexing method integrating prior information correction and iterative refinement in protein crystallography

Qiang Zhou et al.

Summary: A new multi-lattice indexing method based on whole-pattern matching principle has been proposed for accurately identifying multiple crystal lattices in macromolecular crystallography. The method features local correction and iterative refinement, which are critical for processing multi-crystal data sets. Careful exclusion of overlapping reflections before scaling is confirmed to guarantee accurate data reduction results.

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES (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 Multidisciplinary Sciences

Ultracompact 3D microfluidics for time-resolved structural biology

Juraj Knoska et al.

NATURE COMMUNICATIONS (2020)

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Article Chemistry, Multidisciplinary

3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow

Diana C. F. Monteiro et al.

IUCRJ (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, Physical

JUNGFRAU detector for brighter x-ray sources: Solutions for IT and data science challenges in macromolecular crystallography

Filip Leonarski et al.

STRUCTURAL DYNAMICS-US (2020)

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Article Chemistry, Multidisciplinary

SPIND-TC: an indexing method for two-color X-ray diffraction data

Xuanxuan Li et al.

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES (2020)

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Article Chemistry, Multidisciplinary

Viscous-medium-based crystal support in a sample holder for fixed-target serial femtosecond crystallography

Keondo 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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Article Crystallography

Fixed-Target Serial Synchrotron Crystallography Using Nylon Mesh and Enclosed Film-Based Sample Holder

Suk-Youl Park et al.

CRYSTALS (2020)

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Article Biochemistry & Molecular Biology

Serial synchrotron crystallography for time-resolved structural biology

Arwen R. Pearson et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)

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Article Biochemistry & Molecular Biology

Recent results in time resolved serial femtosecond crystallography at XFELs

Allen M. Orville

CURRENT OPINION IN STRUCTURAL BIOLOGY (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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Review Biochemistry & Molecular Biology

Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources

Marius Schmidt

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 Chemistry, Multidisciplinary

XGANDALF - extended gradient descent algorithm for lattice finding

Yaroslav Gevorkov et al.

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES (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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Proceedings Paper Instruments & Instrumentation

Percival: a Soft X-Ray Imager for Synchrotron Rings and Free Electron Lasers

Alessandro Marras et al.

13TH INTERNATIONAL CONFERENCE ON SYNCHROTRON RADIATION INSTRUMENTATION (SRI2018) (2019)

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Article Biochemical Research Methods

The hit-and-return system enables efficient time-resolved serial synchrotron crystallography

Eike C. Schulz et al.

NATURE METHODS (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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Article Chemistry, Multidisciplinary

Mix-and-diffuse serial synchrotron crystallography

Kenneth R. Beyerlein et al.

IUCRJ (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 Microscopy

Data systems for the Linac coherent light source

J. Thayer et al.

ADVANCED STRUCTURAL AND CHEMICAL IMAGING (2017)

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Article Chemistry, Multidisciplinary

Recent developments in CrystFEL

Thomas A. White et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2016)

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Article Optics

Accurate determination of segmented X-ray detector geometry

Oleksandr Yefanov et al.

OPTICS EXPRESS (2015)

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Article Biochemical Research Methods

A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

Thomas D. Murray et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2015)

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Article Biochemical Research Methods

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

Nicolas Coquelle et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2015)

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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 Instruments & Instrumentation

Development of an X-ray pixel detector with multi-port charge-coupled device for X-ray free-electron laser experiments

Takashi Kameshima et al.

REVIEW OF SCIENTIFIC INSTRUMENTS (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 Multidisciplinary Sciences

Fixed-target protein serial microcrystallography with an x-ray free electron laser

Mark S. Hunter et al.

SCIENTIFIC REPORTS (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 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 Physics, Applied

Gas dynamic virtual nozzle for generation of microscopic droplet streams

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JOURNAL OF PHYSICS D-APPLIED PHYSICS (2008)

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Hit and Indexing Rate in Serial Crystallography: Incomparable Statistics

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