Acta Crystallographica Section D-Structural Biology

Article	Citations
Utilizing anomalous signals for element identification in macromolecular crystallography	411
EMinsight: a tool to capture cryoEM microscope configuration and experimental outcomes for analysis and deposition	209
Slice'N'Dice: maximizing the value of predicted models for structural biologists	83
A web-based dashboard for RELION metadata visualization	56
New insights into the domain of unknown function (DUF) of EccC5, the pivotal ATPase providing the secretion driving force to the ESX-5 secretion system	51
Michaelis-like complex of mouse ketohexokinase isoform C	49
Racemic crystal structures of A-DNA duplexes	46
SCOMAP-XD: atomistic deuterium contrast matching for small-angle neutron scattering in biology	43
The impact of folding modes and deuteration on the atomic resolution structure of hen egg-white lysozyme	39
Using graphlet degree vectors to predict atomic displacement parameters in protein structures	38
Current trends in macromolecular model refinement and validation	37
The TR-icOS setup at the ESRF: time-resolved microsecond UV–Vis absorption spectroscopy on protein crystals	35
CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures	34
Room-temperature serial synchrotron crystallography of Drosophila cryptochrome	32
Structure of a hydrophobic leucinostatin derivative determined by host lattice display	30
Structure-based discovery of an antipsychotic drug, paliperidone, as a modulator of human superoxide dismutase 1: a potential therapeutic target in amyotrophic lateral sclerosis	26
Glycoside hydrolase subfamily GH5_57 features a highly redesigned catalytic interface to process complex hetero-β-mannans	26
Unravelling the secrets of multi-domain lytic polysaccharide monooxygenases (LPMOs)	24
Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM	24
Structural and biochemical insights into purine-based drug molecules in hBRD2 delineate a unique binding mode opening new vistas in the design of inhibitors of the BET family	24
Near-atomic resolution reconstructions from in situ revitrified cryo samples	23
Protonation states of hen egg-white lysozyme observed using D/H contrast neutron crystallography	21
Crystallization, structural characterization and kinetic analysis of a GH26 β-mannanase from Klebsiella oxytoca KUB-CW2-3	21
A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography	21
Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum. Corrigendum	20

Structural and functional studies of SAV1707 from Staphylococcus aureus elucidate its distinct metal-dependent activity and a crucial residue for catalysis	20
Structural insights into the interaction of papain-like protease 2 from the alphacoronavirus porcine epidemic diarrhea virus and ubiquitin	19
Modelling covalent linkages in CCP4	18
The structure ofPhocaeicola vulgatussialic acid acetylesterase	17
Control of strain in subgrains of protein crystals by the introduction of grown-in dislocations	17
Databases for intrinsically disordered proteins	15
Predicting the performance of automated crystallographic model-building pipelines	15
Structural basis of ligand recognition and transport by Sfh2, a yeast phosphatidylinositol transfer protein of the Sec14 superfamily	15
Validation, analysis and annotation of cryo-EM structures	14
Optimized cryo-EM data-acquisition workflow by sample-thickness determination	14
Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6	14
α-SAS: an integrative approach for structural modeling of biological macromolecules in solution	14
Are the St John's wort Hyp-1 superstructures different?	14
Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM	13
B-factor accuracy in protein crystal structures	13
Native glycosylation and binding of the antidepressant paroxetine in a low-resolution crystal structure of human myeloperoxidase	13
Dependence of crystallographic atomic displacement parameters on temperature (25–150 K) for complexes of horse liver alcohol dehydrogenase	13
Determination of intracellular protein–ligand binding affinity by competition binding in-cell NMR	13
Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion	13
Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects	13
Towards the automatic crystal structure solution of nucleic acids: automated model building using the new CAB program	13
Likelihood-based interactive local docking into cryo-EM maps in ChimeraX	12
Hydrogen-bond-driven supramolecular helical assembly of a coumarin-substituted phthalonitrile derivative: synthesis andin vitroanticancer activity against colorectal adenocarcinoma	12
Factors affecting macromolecule orientations in thin films formed in cryo-EM	12
Comparison of two crystal polymorphs of NowGFP reveals a new conformational state trapped by crystal packing	12
EMhub: a web platform for data management and on-the-fly processing in scientific facilities	11
Structural basis for substrate recognition in the Phytolacca americana glycosyltransferase PaGT3	11
Analysis of crystallographic phase retrieval using iterative projection algorithms	11
Neutron crystallographic refinement with REFMAC5 from the CCP4 suite	11
Peter Main (1939–2024)	11
New restraints and validation approaches for nucleic acid structures in PDB-REDO	11
xia2.multiplex: a multi-crystal data-analysis pipeline	11
VitroJet: new features and case studies	10
Accelerating crystal structure determination with iterative AlphaFold prediction	10
Structural dynamics: review of time-resolved cryo-EM	10
Tomo Live: an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows	10
New system for archiving integrative structures	10
Structural visualization of transient interactions between the cis-acting acyltransferase and acyl carrier protein of the salinomycin modular polyketide synthase	10
Improving macromolecular structure refinement with metal-coordination restraints	10
MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more	10
Jan Drenth (1925–2025)	10
Structural characterization of the ACDC domain from ApiAP2 proteins, a potential molecular target against apicomplexan parasites	9
Crystal-packing analysis of translation initiation factor 2 reveals new details of its function	9
Polyelectrolyte coating of cryo-EM grids improves lateral distribution and prevents aggregation of macromolecules	9
High-confidence placement of low-occupancy fragments into electron density using the anomalous signal of sulfur and halogen atoms	9
Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family	9
The ManifoldEM method for cryo-EM: a step-by-step breakdown accompanied by a modern Python implementation	9
X-ray diffraction and in vivo studies reveal the quinary structure of Trypanosoma cruzi nucleoside diphosphate kinase 1: a novel helical oligomer structure	8
Photosystem II: light-dependent oscillation of ligand composition at its active site	8
Crystal and solution structures of a novel antimicrobial peptide fromChrysomya megacephala	8

Intracellular drug binding affinities by NMR	8
Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation	8
Development of CryoVR, a virtual reality training system for hands-on cryoEM operations	7
Structural and spectrophotometric investigation of two unnatural amino-acid altered chromophores in the superfolder green fluorescent protein	7
Intermediates in allosteric equilibria of DnaK–ATP interactions with substrate peptides	7
Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae	7
Data collection from crystals grown in microfluidic droplets	7
Two states of a light-sensitive membrane protein captured at room temperature using thin-film sample mounts	7
The crystal structure of CbpD clarifies substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases	7
Structural insights into choline-O-sulfatase reveal the molecular determinants for ligand binding	7
Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography	7
Structure of the plant growth-promoting factor YxaL from the rhizobacterium Bacillus velezensis and its application to protein engineering	7
Radiation-induced defects in protein crystals observed by X-ray topography	7
Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation–π interaction	7
Conformation-dependent ligand hot spots in the spliceosomal RNA helicase BRR2	6
Structural and binding studies of a new chitin-active AA10 lytic polysaccharide monooxygenase from the marine bacterium Vibrio campbellii	6
Structure–function studies of a novel laccase-like multicopper oxidase fromThermothelomyces thermophilaprovide insights into its biological role	6
Kinetic and structural studies of the reaction of Escherichia coli dihydrodipicolinate synthase with (S)-2-bromopropionate	6
Neutralization of the anthrax toxin by antibody-mediated stapling of its membrane-penetrating loop	6
Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase	6
Correcting systematic errors in diffraction data with modern scaling algorithms	6
Structural basis for the allosteric pathway of 4-amino-4-deoxychorismate synthase	6
Crystal structure of DNA polymerase I from Thermus phage G20c	6
Synergic action of an inserted carbohydrate-binding module in a glycoside hydrolase family 5 endoglucanase	6
Structure of reverse gyrase with a minimal latch that supports ATP-dependent positive supercoiling without specific interactions with the topoisomerase domain	6
Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum	6
A scalable strategy to solve structures of PDZ domains and their complexes	6
Raimond B. G. Ravelli (25 March 1968–30 June 2023)	6
Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization	5
Direct calculation of cryo-EM and crystallographic model maps for real-space refinement	5
Buccaneer model building with neural network fragment selection	5
Notes of a protein crystallographer: the legacy of J.-B. J. Fourier – crystallography, time and beyond	5
Anaerobic fixed-target serial crystallography using sandwiched silicon nitride membranes	5
Robust and automatic beamstop shadow outlier rejection: combining crystallographic statistics with modern clustering under a semi-supervised learning strategy	5
Errors in structural biology are not the exception	5
Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7	5
HEIDI: an experiment-management platform enabling high-throughput fragment and compound screening	5
Identifying and avoiding radiation damage in macromolecular crystallography	5
Advanced exploitation of unmerged reflection data during processing and refinement with autoPROC and BUSTER	5
The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF	5
Updated restraint dictionaries for carbohydrates in the pyranose form	5
Cryo-EM structure of adeno-associated virus 4 at 2.2 Å resolution	5
30 years of Acta D	5
Structures of permuted halves of a modern ribose-binding protein	5
A tetramerization domain in prokaryotic and eukaryotic transcription regulators homologous to p53	5
Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals	5
The future of biomolecular simulation in the pharmaceutical industry: what we can learn from aerodynamics modelling and weather prediction. Part 1. understanding the physical and computational complex	5
The BAM7 gene in Zea mays encodes a protein with similar structural and catalytic properties to Arabidopsis BAM2	4
UnityMol prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments	4
Duplicate entries in the Protein Data Bank: how to detect and handle them	4
Implications of AlphaFold2 for crystallographic phasing by molecular replacement	4
Structural flexibility of Toscana virus nucleoprotein in the presence of a single-chain camelid antibody	4
Structure and stability of an apo thermophilic esterase that hydrolyzes polyhydroxybutyrate	4
Structural basis for the fast maturation of pcStar, a photoconvertible fluorescent protein	4
Likelihood-based signal and noise analysis for docking of models into cryo-EM maps	4
InstaMap: instant-NGP for cryo-EM density maps	4
Structure of human factor VIIa–soluble tissue factor with calcium, magnesium and rubidium	4
TomoCPT: a generalizable model for 3D particle detection and localization in cryo-electron tomograms	4
2023 update of template tables for reporting biomolecular structural modelling of small-angle scattering data	4
Restoration of the 3D structure of insect flight muscle from a rotationally averaged 2D X-ray diffraction pattern	4
Exploring ligand dynamics in protein crystal structures with ensemble refinement	4
On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy	4
Reconsideration of the P-clusters in VFe proteins using the bond-valence method: towards their electron transfer and protonation	4
Integrated sample-handling and mounting system for fixed-target serial synchrotron crystallography	3
From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons	3
Crystal structures of a dodecameric multicopper oxidase from Marinithermus hydrothermalis	3
John D. Westbrook Jr (1957–2021)	3
The three-dimensional structure of Drosophila melanogaster (6–4) photolyase at room temperature	3
Crystal structure of the ferredoxin reductase component of carbazole 1,9a-dioxygenase from Janthinobacterium sp. J3	3
Highlighting the factors governing transglycosylation in the GH5_5 endo-1,4-β-glucanase RBcel1	3
Structural and biochemical analyses of the tetrameric carboxypeptidase S9Cfn from Fusobacterium nucleatum	3
Structural basis of chitin utilization by a GH20 β-N-acetylglucosaminidase from Vibrio campbellii strain ATCC BAA-1116	3
The structure and molecular dynamics of prolyl oligopeptidase from Microbulbifer arenaceous provide insights into catalytic and regulatory mechanisms	3
Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum	3
Atomic model validation using the CCP-EM software suite	3
On the suitability of using the diagonal Gaussian approximation in the calculation of the magnitude-based likelihood function	3
Principal component analysis is limited to low-resolution analysis in cryoEM	3
A radical approach to radicals	3
A rush to explore protein–ligand electrostatic interaction energy with Charger	3
Has AlphaFold3 achieved success for RNA?	3

Single-support serial isomorphous replacement phasing	3
Structure and metal-binding properties of PA4063, a novel player in periplasmic zinc trafficking byPseudomonas aeruginosa	3
Correlative cryo-imaging of the cellular universe with soft X-rays and laser light used to track F-actin structures in mammalian cells	3
Structural analysis of LpqY, a substrate-binding protein from the SugABC transporter of Mycobacterium tuberculosis, provides insights into its trehalose specificity	3
High-resolution structures of the bound effectors avadomide (CC-122) and iberdomide (CC-220) highlight advantages and limitations of the MsCI4 soaking system	3
A recurring packing contact in crystals of InlB pinpoints functional binding sites in the internalin domain and the B repeat	3
Cocrystallization of ubiquitin–deubiquitinase complexes through disulfide linkage	2
Crystal structures of human and mouse ketohexokinase provide a structural basis for species- and isoform-selective inhibitor design	2
Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score	2
Serial femtosecond X-ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase	2
Structural and functional identification of the uncharacterized metallo-β-lactamase superfamily protein TW9814 as a phosphodiesterase with unique metal coordination	2
The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1	2
The impact of oncogenic mutations of the viral Src kinase on the structure and stability of the SH3 domain	2
The impact of molecular variants, crystallization conditions and the space group on ligand–protein complexes: a case study on bacterial phosphotriesterase	2
Module walking using an SH3-like cell-wall-binding domain leads to a new GH184 family of muramidases	2
Dynamics and Kinetics in Structural Biology: Unravelling Function Through Time-Resolved Structural Analysis. By Keith Moffat and Eaton E. Lattman. Wiley, New York, 2023, pp. 288. ISBN 978-1-119	2
Welcoming five new Co-editors	2
K-edge anomalous SAXS for protein solution structure modeling	2
A service-based approach to cryoEM facility processing pipelines at eBIC	2
Predicted models and CCP4	2
Introduction to the virtual thematic issue on room-temperature biological crystallography	2
Crystal structure of a novel homodimericD-allulose 3-epimerase from a Clostridia bacterium	2
Crystal structure of a covalently linked Aurora-A–MYCN complex	2
Structural and functional investigation of the human snRNP assembly factor AAR2 in complex with the RNase H-like domain of PRPF8	2
Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection	2
Raw diffraction data are our ground truth from which all subsequent workflows develop	2
Crystallographic and X-ray scattering study of RdfS, a recombination directionality factor from an integrative and conjugative element	2
CHiMP: deep-learning tools trained on protein crystallization micrographs to enable automation of experiments	2
Protein–macrocycle polymorphism: crystal form IV of the Ralstonia solanacearum lectin–sulfonato-calix[8]arene complex	2
Domain structure and cross-linking in a giant adhesin from the Mobiluncus mulieris bacterium	2
XFEL structure of carbonic anhydrase II: a comparative study of XFEL, NMR, X-ray and neutron structures	2
Overall protein structure quality assessment using hydrogen-bonding parameters	2
The structure of the RBD–E77 Fab complex reveals neutralization and immune escape of SARS-CoV-2	2
Cysteine synthase: multiple structures of a key enzyme in cysteine synthesis and a potential drug target for Chagas disease and leishmaniasis	2
Structural and thermodynamic insights into a novel Mg2+–citrate-binding protein from the ABC transporter superfamily	2
Drosophila melanogaster frataxin: protein crystal and predicted solution structure with identification of the iron-binding regions	2
Training undergraduate research assistants with an outcome-oriented and skill-based mentoring strategy	2
Welcoming two new Co-editors	2
The crystal structure of the N-terminal domain of the backbone pilin LrpA reveals a new closure-and-twist motion for assembling dynamic pili in Ligilactobacillus ruminis	2
Mechanism-based cross-linking probes capture the Escherichia coli ketosynthase FabB in conformationally distinct catalytic states	2
Managing macromolecular crystallographic data with a laboratory information management system	2
An alternative conformation of the N-terminal loop of human dihydroorotate dehydrogenase drives binding to a potent antiproliferative agent	2
Continuous development in macromolecular crystallography with CCP4	2
Efficient in situ screening of and data collection from microcrystals in crystallization plates	2
Novel starting points for fragment-based drug design against mycobacterial thioredoxin reductase identified using crystallographic fragment screening	2
Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis	1
Right-handed Z-DNA at ultrahigh resolution: a tale of two hands and the power of the crystallographic method	1
Introduction to molecular replacement: a time perspective	1
Mamannamana Vijayan (1941–2022)	1
Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap	1
Cryo-EM single-particle structure refinement and map calculation usingServalcat	1
Making the most of an abundance of data	1
Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain	1
Improved joint X-ray and neutron refinement procedure in Phenix	1
Structural basis of regioselective tryptophan dibromination by the single-component flavin-dependent halogenase AetF	1
A database overview of metal-coordination distances in metalloproteins	1
Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0	1
Structural and functional characterization of a thermostable secretory phospholipase A2 from Sciscionella marina and its application in liposome biotransformation	1
The success rate of processed predicted models in molecular replacement: implications for experimental phasing in the AlphaFold era	1
FragMAXapp: crystallographic fragment-screening data-analysis and project-management system	1
A small step towards an important goal: fragment screen of the c-di-AMP-synthesizing enzyme CdaA	1
Structural and biochemical characterization of the novel serpin Iripin-5 from Ixodes ricinus	1
STOPGAP: an open-source package for template matching, subtomogram alignment and classification	1
AutoPX: a new software package to process X-ray diffraction data from biomacromolecular crystals	1
Scaling and merging macromolecular diffuse scattering with mdx2	1
Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures	1
X-ray structure of the metastable SEPT14–SEPT7 coiled coil reveals a hendecad region crucial for heterodimerization	1
Zymogenic latency in an ∼250-million-year-old astacin metallopeptidase	1
Post-translational modifications in the Protein Data Bank	1
Analysis and validation of overall N-glycan conformation in Privateer	1
Expansion of the diversity of dispersin scaffolds	1
Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions	1
Modes and model building in SHELXE	1
LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments	1
Structural and functional characterization of the novel endo-α(1,4)-fucoidanase Mef1 from the marine bacterium Muricauda eckloniae	1