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Case-controlled structure validation.
Although many factors influence the quality of a macromolecular crystal structure, validation criteria are usually only calibrated using one of these factors, the resolution. For many purposes this is sufficient, but there are...
Improvement of molecular-replacement models with Sculptor.
In molecular replacement, the quality of models can be improved by transferring information contained in sequence alignment to the template structure. A family of algorithms has been developed that make use of the...
Maximum-likelihood determination of anomalous substructures.
A fast Fourier transform (FFT) method is described for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by X-ray single-wavelength anomalous...
Experimental phasing
Developments in protein crystal structure determination by experimental phasing are reviewed, emphasizing the theoretical continuum between experimental phasing, density modification, model building and refinement. Traditional...
Adaptive Cartesian and torsional restraints for interactive model rebuilding.
When building atomic models into weak and/or low-resolution density, a common strategy is to restrain their conformation to that of a higher resolution model of the same or similar sequence. When doing so, it is important to...
Structural basis for the specificity of renin-mediated angiotensinogen cleavage.
The renin-angiotensin cascade is a hormone system that regulates blood pressure and fluid balance. Renin-mediated cleavage of the angiotensin I peptide from the N terminus of angiotensinogen (AGT) is the rate-limiting step of...
Improved estimates of coordinate error for molecular replacement.
The estimate of the root-mean-square deviation (r.m.s.d.) in coordinates between the model and the target is an essential parameter for calibrating likelihood functions for molecular replacement (MR). Good estimates of the...
Measuring and using information gained by observing diffraction data.
The information gained by making a measurement, termed the Kullback-Leibler divergence, assesses how much more precisely the true quantity is known after the measurement was made (the posterior probability distribution) than...
Using SAD data in Phaser.
Phaser is a program that implements likelihood-based methods to solve macromolecular crystal structures, currently by molecular replacement or single-wavelength anomalous diffraction (SAD). SAD phasing is based on a likelihood...
Angiotensinogen and the Modulation of Blood Pressure.
The angiotensin peptides that control blood pressure are released from the non-inhibitory plasma serpin, angiotensinogen, on cleavage of its extended N-terminal tail by the specific aspartyl-protease, renin. Angiotensinogen had...
Likelihood‐based estimation of substructure content from single‐wavelength anomalous diffraction (SAD) intensity data
SAD phasing can be challenging when the signal‐to‐noise ratio is low. In such cases, having an accurate estimate of the substructure content can determine whether or not the substructure of anomalous scatterer positions can...
Likelihood-based signal and noise analysis for docking of models into cryo-EM maps.
Fast, reliable docking of models into cryo-EM maps requires understanding of the errors in the maps and the models. Likelihood-based approaches to errors have proven to be powerful and adaptable in experimental structural...
Improving experimental phases for strong reflections prior to density modification.
Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so...
Likelihood-based docking of models into cryo-EM maps.
Optimized docking of models into cryo-EM maps requires exploiting an understanding of the signal expected in the data to minimize the calculation time while maintaining sufficient signal. The likelihood-based rotation function...
Likelihood-based estimation of substructure content from single-wavelength anomalous diffraction (SAD) intensity data.
SAD phasing can be challenging when the signal-to-noise ratio is low. In such cases, having an accurate estimate of the substructure content can determine whether or not the substructure of anomalous scatterer positions can...
Structure and oligomerization of the periplasmic domain of GspL from the type II secretion system of Pseudomonas aeruginosa.
The ability of bacteria to infect a host relies in part on the secretion of molecular virulence factors across the cell envelope. Pseudomonas aeruginosa, a ubiquitous environmental bacterium causing opportunistic infections in...
Implications of AlphaFold2 for crystallographic phasing by molecular replacement.
The AlphaFold2 results in the 14th edition of Critical Assessment of Structure Prediction (CASP14) showed that accurate (low root-mean-square deviation) in silico models of protein structure domains are on the horizon, whether...
Towards engineering hormone-binding globulins as drug delivery agents.
Amino Acid Sequence Biological Transport Crystallography X-Ray Drug Carriers Escherichia coli Fluoresceins Gene Expression Humans Hydrocortisone Leukocyte Elastase Models Molecular Molecular Sequence Data Molecular Targeted Therapy Mutation Prostate-specific antigen Protein Engineering Protein Structure Secondary Recombinant Proteins Thrombin Thyroxine Transcortin
Evaluation of template-based modeling in CASP13.
Performance in the template-based modeling (TBM) category of CASP13 is assessed here, using a variety of metrics. Performance of the predictor groups that participated is ranked using the primary ranking score that was developed...
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