Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection - PubMed The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in…

News Alert: We've updated SBGrid's primary citation to our 2024 Acta Crystallographica paper. We would be grateful if you could use this reference in future manuscripts, preprints, and related work where appropriate.

Read it here: buff.ly/RQ0Ybpx

#SBGrid #Citation

Take a look at our March issue: journals.iucr.org/d/issues/202...

On the cover: the response of two paradigmatic metalloproteins of different types, one iron-containing and one copper-containing, to X-ray-induced metal reduction at cryo- and room temperature journals.iucr.org/d/issues/202...

Q-score as a reliability measure for atomic coordinate models

Q-scores are calculated for atomic models derived from 3D electron microscopy maps, measure how well the model fits the map and reflect the quality of the map itself.

🔗 Find out more:
https://ow.ly/4Vkx50Ynrxi

@ucsandiego @ActaCrystD @IUCr #CryoEM #QScores #Validation

PDB Reaches a New Milestone The PDB now contains more than 250,000 entries

PDB Reaches a New Milestone: more than 250,000 entries

Radiation-dose effects in correlative X-ray/cryo-electron microscopy of frozen-hydrated biological samples Cryo-EM analysis of apoferritin exposed to an X-ray dose of 100 MGy confirms the potential for high-resolution correlative imaging workflows combining X-ray tomography and cryo-EM.

Thorsten B. Blum et al.: Radiation-dose effects in correlative X-ray/cryo-electron microscopy of frozen-hydrated biological samples #CryoXRayTomography #CryoElectronMicroscopy #CorrelativeMicroscopy @eth...#IUCr https://journals.iucr.org/paper?S2059798326001427

An optimized data-acquisition and processing strategy for the collection of high-quality electron diffraction data from extended crystals using conventional cryo-EM instrumentation #ElectronDiffraction #RadiationDamage #DataCompleteness doi.org/10.1107/S205...

This topical review considers a Protein Data Bank and Cambridge Structural Database data survey of crystal structures that have been determined at elevated temperatures #BodyTemperature #PhysiologicalConditions #37C doi.org/10.1107/S205...

A theoretical framework for the development of dynamic nuclear polarization neutron macromolecular crystallography to advance the resolution of H atoms within biomolecular crystals is presented #DynamicNuclearPolarization #PhaseRetrieval #Hydrogen doi.org/10.1107/S205...

X-ray beam effects on metallo-peptides reflect redox events: insights from X-ray absorption spectroscopy measurements on metal complexes of truncated amyloid-β peptides X-ray exposure influences the structures of Cu(I), Cu(II) and Zn(II) complexes of amyloid-β (Aβ) peptides in different ways. While Cu(I) and Zn(II) complexes show no detectable X-ray-induced spectral changes, Cu(II) complexes undergo significant spectral evolution under irradiation. Experiments on the truncated fragments Aβ1–6 and Aβ1–16 show that the extent of relaxation depends on the peptide length, on the binding mode and on the temperature.

Bharath Vinjamuri et al.: X-ray beam effects on metallo-peptides reflect redox events: insights from X-ray absorption spectroscopy measurements on metal complexes of truncated amyloid-β peptides @UGrenobleAlpes...#IUCr https://journals.iucr.org/paper?S2059798326001348

Having made the transition from primarily X-ray crystallography to cryoEM, this resource would have been invaluable.

This is a fantastic example of how to begin as a newcomer to #cryoEM. Being proactive in getting advice from experienced scientists and going to any of the great workshops would likely lower the incidences of erroneous structures in the EMDB and PDB (There’s not a lot but there are a few).

This is an interesting article for those beginning down the cryoEM route for structure determination from the perspective of a crystallography lab. Not giving up on crystallography yet 😜 but I honestly can't think of a single crystallography lab now that isn't also using CryoEM in some capacity.

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements Cryo-ET is a rapidly emerging technique that enables 3D visualization of complex biological structures, but present limits on signal-to-noise ratio and reconstruction quality pose challenges for downstream analysis. Here, we present a systematic analysis of state-of-the-art deep-learning methods for contrast enhancement and propose improvements in neural network architectures and training objectives to preserve more high-resolution information.

Henry N. Jones et al.: Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements #ContrastEnhancement ... #IUCr https://journals.iucr.org/paper?S2059798326001166

Breaking barriers: transitioning from X-ray crystallography to cryo-EM for structural studies This article describes the transition of the Glass laboratory from X-ray crystallography to single-particle cryo-electron microscopy (cryo-EM) for structural studies of ATAD2B, a large AAA+ ATPase- and bromodomain-containing protein involved in chromatin regulation. It outlines practical strategies for protein expression, sample preparation, data processing and model building, offering a comprehensive workflow and troubleshooting guide for new cryo-EM users working with large, flexible macromolecular complexes.

Hassan Zafar et al.: Breaking barriers: transitioning from X-ray crystallography to cryo-EM for structural studies #CryoElectronMicroscopyCryoEM #StructuralBiology #SingleParticleAnalysis @uvmvermont...#IUCr https://journals.iucr.org/paper?S205979832600080X

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements Cryo-ET is a rapidly emerging technique that enables 3D visualization of complex biological structures, but present limits on signal-to-noise ratio and reconstruction quality pose challenges for downstream analysis. Here, we present a systematic analysis of state-of-the-art deep-learning methods for contrast enhancement and propose improvements in neural network architectures and training objectives to preserve more high-resolution information.

Henry N. Jones et al.: Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements #ContrastEnhancement ... #IUCr https://journals.iucr.org/paper?S2059798326001166

Breaking barriers: transitioning from X-ray crystallography to cryo-EM for structural studies This article describes the transition of the Glass laboratory from X-ray crystallography to single-particle cryo-electron microscopy (cryo-EM) for structural studies of ATAD2B, a large AAA+ ATPase- and bromodomain-containing protein involved in chromatin regulation. It outlines practical strategies for protein expression, sample preparation, data processing and model building, offering a comprehensive workflow and troubleshooting guide for new cryo-EM users working with large, flexible macromolecular complexes.

Hassan Zafar et al.: Breaking barriers: transitioning from X-ray crystallography to cryo-EM for structural studies #CryoElectronMicroscopyCryoEM #StructuralBiology #SingleParticleAnalysis @uvmvermont...#IUCr https://journals.iucr.org/paper?S205979832600080X

A protocol has been developed to quantify and localize questionable backbone conformations in X-ray structure models, which can affect the interpretation of structural data #QuestionableConformations #CrystallographicStructures #StructuralAlphabet doi.org/10.1107/S205...

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields A database of validated ligand restraints computed using various levels of quantum mechanics is generated and distributed with Phenix to streamline and improve macromolecular refinement results.

Nigel W. Moriarty et al.: Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields #MacromolecularCrystallography #LigandRestraints #Refinement @UCBerkeley...#IUCr https://journals.iucr.org/paper?S2059798326000975

Modification of PLK1 following the surface-entropy reduction approach yielded a protein which crystallizes readily and forms an excellent new crystallization platform for PLK1–inhibitor co-crystal structures #SurfaceEntropyReduction #SER #Kinase doi.org/10.1107/S205...

Phosphatidylinositol transfer protein α binds microcolins in its open conformation We report the crystal structure of human PITPα in complex with microcolin H at 2.0 Å resolution, revealing that microcolins bind covalently within the lipid-binding cavity and stabilize PITPα in an open conformation with a markedly enlarged cavity relative to the lipid-bound state. These results define the structural basis of PITP inhibition by microcolins and underscore the importance of using ligand-bound conformations for accurate structure-based modeling.

Andrea Eisenreichova et al.: Phosphatidylinositol transfer protein α binds microcolins in its open conformation #LipidTransport #CrystalStructure #Inhibitor ... #IUCr https://journals.iucr.org/paper?S2059798326000872

Apo and complex crystal structures of L. reuteri glycosyltransferase C reveal key sugar-nucleotide binding residues underpinning strain-specific glycosylation of serine-rich repeat proteins #AccessorySecretionSystems #Glycosyltransferases doi.org/10.1107/S205...

Using only the first few frames of data from a large number of randomly oriented crystals can improve the recorded ED intensities, the data statistics and the resolution of the final structure #MicroED #DataProcessing #MacromolecularStructure doi.org/10.1107/S205...

Coupled on-line in crystallo UV–Vis absorption spectroscopy and X-ray crystallography to compare specific radiation damage in metal-containing proteins at room versus cryogenic temperature We used on-line in crystallo UV–Vis absorption spectroscopy in conjunction with X-ray crystallography on beamline BM07-FIP2 at the ESRF to compare the structural effects of specific radiation damage o...

I'm proud to present this first article from my PostDoc: We probed the different responses of metalloproteins (myoglobin, Mb and a copper-containing Nitrite Reductase, CuNIR) to reduction of their metal centres by X-rays at two temperatures (100K, 392K-RT) with UV-vis absorption and diffraction.

I find Airlie’s composite self rotation representation much easier to interpret. Check it out!

How X-rays and crystals revealed the true nature of things - NobelPrize.org The story behind the 100-year-old discovery that continues to render Nobel Prizes.

Very excited to share my love of crystallography in this article celebrating over 100 years of X-ray methods and the Nobel Prize for BBC and the Nobel Foundation:

www.nobelprize.org/stories/x-ra...

Modelling of radiation damage and beam-induced heating of room-temperature samples at extremely high flux MX beamlines Modelling of radiation damage and beam-induced heating at extremely high flux macromolecular crystallography beamlines is presented.

M​artin V. Appleby et al.: Modelling of radiation damage and beam-induced heating of room-temperature samples at extremely high flux MX beamlines #RadiationDamage #MacromolecularCrystallography ... #IUCr https://journals.iucr.org/paper?S2052252525011224

The Xtricorder tool offers a likelihood-enhanced self-rotation function and presents a novel graphical representation, the `composite-section diagram' #MolecularReplacement #MatthewsCoefficient #MachineLearning doi.org/10.1107/S205...

CrysFormer is a machine-learning (ML)-based approach for improving predictions provided by other ML models, i.e. those in the AlphaFold Protein Structure Database, given Patterson maps #Phasing #Patterson #MachineLearning doi.org/10.1107/S205...

CryoLike is computationally efficient software for evaluating image-to-structure (or image-to-volume) likelihoods across large image data sets packaged in a user-friendly Python workflow #CryoEM #MolecularModeling #MolecularDynamics doi.org/10.1107/S205...

Updating direct methods V. Phasing when triplet invariants are estimated via the Patterson map Crystal structures of proteins and nucleic acids with data resolution up to 2.2 Å are solved via a novel direct-methods program using the Pattterson map as prior information.

M​aria Cristina Burla et al.: Updating direct methods V. Phasing when triplet invariants are estimated via the Patterson map #DirectMethods #PattersonMap #ProbabilisticApproach ... #IUCr https://journals.iucr.org/paper?S2059798326000732