4.4 Article

Linking B-factor and temperature-induced conformational transition

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

The reproducible normality of the crystallographic B-factor

Natalia Goncalves Ramos et al.

Summary: This study evaluated the reproducibility of uncertainties in protein crystallography and found that empirical scaling/normalization can result in reproducible B-factors.

ANALYTICAL BIOCHEMISTRY (2022)

Letter Multidisciplinary Sciences

The protein-folding problem: Not yet solved

Peter B. Moore et al.

SCIENCE (2022)

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)

Article Biochemical Research Methods

B-factor accuracy in protein crystal structures

Oliviero Carugo

Summary: The accuracy of B factors in protein crystal structures has been found to have large errors, comparable to values estimated two decades ago. Normalizing B factors is still essential when comparing different crystal structures. Novel experimental and computational tools are needed for improved quantitative analysis of raw B factors.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2022)

Editorial Material Multidisciplinary Sciences

Proteins, proteins everywhere

H. Holden Thorp

SCIENCE (2021)

Article Biochemistry & Molecular Biology

Biophysical characterization of two commercially available preparations of the drug containing Escherichia coli L-Asparaginase 2

Talita Stelling de Araujo et al.

Summary: The hydrolysis of asparagine and glutamine by L-asparaginase has been used in treating acute lymphoblastic leukemia for over four decades. A comparative study of two commercially available preparations of the drug containing Escherichia coli L-Asparaginase 2 (EcA2) showed that the presence of L-Asp in the Aginasa formulation provides resistance to in vitro proteolysis for EcA2. Additionally, the study revealed the oligomeric landscape and conformational diversity of EcA2, as well as insights into ligand recognition by the enzyme.

BIOPHYSICAL CHEMISTRY (2021)

Letter Biochemistry & Molecular Biology

AlphaFold2 and the future of structural biology

Patrick Cramer

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

Article Biochemical Research Methods

Time-resolved serial femtosecond crystallography at the European XFEL

Suraj Pandey et al.

NATURE METHODS (2020)

Article Multidisciplinary Sciences

Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures

Eugenio de la Mora et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

Shortening injection matrix for serial crystallography

Ki Hyun Nam

SCIENTIFIC REPORTS (2020)

Article Chemistry, Multidisciplinary

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

Ki Hyun Nam

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2020)

Article Biochemical Research Methods

Predicting protein model correctness in Coot using machine learning

Paul S. Bond et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Lard Injection Matrix for Serial Crystallography

Ki Hyun Nam

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Review Cell Biology

The proteostasis network and its decline in ageing

Mark S. Hipp et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)

Article Biochemical Research Methods

Journey to the center of the protein: allostery from multitemperature multiconformer X-ray crystallography

Daniel A. Keedy

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2019)

Article Chemistry, Multidisciplinary

Rigid-body motion is the main source of diffuse scattering in protein crystallography

T. de Klijn et al.

IUCRJ (2019)

Article Multidisciplinary Sciences

Polyacrylamide injection matrix for serial femtosecond crystallography

Jaehyun Park et al.

SCIENTIFIC REPORTS (2019)

Article Biochemical Research Methods

How large B-factors can be in protein crystal structures

Oliviero Carugo

BMC BIOINFORMATICS (2018)

Editorial Material Medicine, General & Internal

The Proposal to Lower P Value Thresholds to .005

John P. A. Ioannidis

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2018)

Article Biochemical Research Methods

Overview of refinement procedures within REFMAC5: utilizing data from different sources

Oleg Kovalevskiy et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2018)

Article Multidisciplinary Sciences

Measuring and modeling diffuse scattering in protein X-ray crystallography

Andrew H. Van Benschoten et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Multidisciplinary Sciences

Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser

Matteo Levantino et al.

NATURE COMMUNICATIONS (2015)

Article Biochemical Research Methods

Grease matrix as a versatile carrier of proteins for serial crystallography

Michihiro Sugahara et al.

NATURE METHODS (2015)

Article Biochemical Research Methods

Conformation-independent structural comparison of macromolecules with ProSMART

Robert A. Nicholls et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2014)

Article Pharmacology & Pharmacy

Structural meta-analysis of regular human insulin in pharmaceutical formulations

Maely P. Favero-Retto et al.

EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS (2013)

Article Biochemical Research Methods

Spatial distribution of radiation damage to crystalline proteins at 25-300 K

Matthew Warkentin et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2012)

Article Biochemical Research Methods

Overview of the CCP4 suite and current developments

Martyn D. Winn et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2011)

Article Multidisciplinary Sciences

Protein dynamical transition at 110 K

Chae Un Kim et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemical Research Methods

Molecular replacement with MOLREP

Alexei Vagin et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemical Research Methods

Initial evaluations of the reproducibility of vapor-diffusion crystallization

Janet Newman et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2007)

Article Biochemical Research Methods

High-throughput phase-diagram mapping via powder diffraction:: a case study of HEWL versus pH

S Basso et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2005)

Article Biochemical Research Methods

Pros and cons of cryocrystallography: should we also collect a room-temperature data set?

KV Dunlop et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2005)

Article Biochemical Research Methods

Choice of data-collection parameters based on statistic modelling

AN Popov et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2003)