Acta Crystallographica Section D-Structural Biology

Article	Citations
Using graphlet degree vectors to predict atomic displacement parameters in protein structures	667
Structure of the Fab fragment of a humanized 5E5 antibody to a cancer-specific Tn-MUC1 epitope	90
EMhub: a web platform for data management and on-the-fly processing in scientific facilities	69
Cryo-EM single-particle analysis expanding towards increasingly native samples	63
Crystallographic fragment screening against SARS-CoV-2 nonstructural protein 1 using the F2X-Entry Screen and a newly developed fragment library	62
Structural visualization of transient interactions between the cis-acting acyltransferase and acyl carrier protein of the salinomycin modular polyketide synthase	59
Completion of partial structures using Patterson maps with the CrysFormer machine-learning model	50
Limiting the effects of radiation damage in MicroED through dose selection during data processing	47
Comparison of two crystal polymorphs of NowGFP reveals a new conformational state trapped by crystal packing	45
Structural flexibility of Toscana virus nucleoprotein in the presence of a single-chain camelid antibody	44
Updated restraint dictionaries for carbohydrates in the pyranose form	39
Crystal structure of DNA polymerase I from Thermus phage G20c	34
Structures of α-galactosaminidases from the CAZy GH114 family and homologs defining a new GH191 family of glycosidases	33
X-ray diffraction and in vivo studies reveal the quinary structure of Trypanosoma cruzi nucleoside diphosphate kinase 1: a novel helical oligomer structure	33
Data collection from crystals grown in microfluidic droplets	30
A scalable strategy to solve structures of PDZ domains and their complexes	25
Critical evaluation of three cryo-EM structures of particulate methane monooxygenase by quantum refinement	23
Structures of permuted halves of a modern ribose-binding protein	23
Identifying and avoiding radiation damage in macromolecular crystallography	23
Structural studies of NAD + -dependent methanol dehydrogenase 1 from Bacillus methanolicus MGA3	22
Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals	19
On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy	19
A recurring packing contact in crystals of InlB pinpoints functional binding sites in the internalin domain and the B repeat	18
The crystal structure of CbpD clarifies substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases	18
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	18

A radical approach to radicals	18
Raw diffraction data are our ground truth from which all subsequent workflows develop	18
Structural characterization of the ACDC domain from ApiAP2 proteins, a potential molecular target against apicomplexan parasites	18
Training undergraduate research assistants with an outcome-oriented and skill-based mentoring strategy	17
Biophysical Chemistry, Second Edition. By Dagmar Klostermeier and Markus G. Rudolph. CRC Press, Boca Raton, 2025, pp. 944. ISBN 9781032060835. Price GBP 57.39 (hardback)	16
Analysis and validation of overall N-glycan conformation in Privateer	16
Validation of helical symmetry parameters in the EMDB	16
An alternative conformation of the N-terminal loop of human dihydroorotate dehydrogenase drives binding to a potent antiproliferative agent	16
Overall protein structure quality assessment using hydrogen-bonding parameters	16
Crystal structure of coagulation factor XII N-terminal domains 1–5	15
Deciphering the crystal structure of a novel nanobody against the NEIL1 DNA glycosylase	15
Statistical analyses of the oxidized P-clusters in MoFe proteins using the bond-valence method: towards their electron transfer in nitrogenases	15
Medical contrast agents as promising tools for biomacromolecular SAXS experiments	14
A high-resolution data set of fatty acid-binding protein structures. III. Unexpectedly high occurrence of wrong ligands	14
Notes of a protein crystallographer: the advantages of combining new integrated methods of structure solution with traditional data visuals	14
Structural and functional analysis of the D-alanyl carrier protein ligase DltA from Staphylococcus aureus Mu50	14
Structural studies of β-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus	14
Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned	14
3D structures of the Plasmodium vivax subtilisin-like drug target SUB1 reveal conformational changes to accommodate a substrate-derived α-ketoamide inhibitor	14
Michael James (1940–2023)	13
Pillar data-acquisition strategies for cryo-electron tomography of beam-sensitive biological samples	13
Alexei Vagin (1944–2023)	13
Secret of Life: Rosalind Franklin, James Watson, Francis Crick, and the discovery of DNA's Double Helix. By Howard Markel. W. W. Norton & Co., 2021. Hardback, pp. 608. ISBN 978-1324002239.	13
The T2 structure of polycrystalline cubic human insulin	13
Structural mechanism of Escherichia coli cyanase	12
Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket	12
Molecular basis of transcriptional repression of anti-CRISPR by anti-CRISPR-associated 2	12
Preparation and characterization of inactivated tick-borne encephalitis virus samples for single-particle imaging at the European XFEL	12
Submission of structural biology data for review purposes	12
Crystal structures of the molecular class A β-lactamase TEM-171 and its complexes with tazobactam	12
Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy	11
Elucidating polymorphs of crystal structures by intensity-based hierarchical clustering analysis of multiple diffraction data sets	11
Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks	11
Direct phasing algorithm for protein crystals with high solvent content using low-resolution diffraction data	11
Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization	11
A new inactive conformation of SARS-CoV-2 main protease	11
Biochemical and structural insights into an unusual, alkali-metal-independent S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803	11
The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study report	11
Best practices for time-resolved serial synchrotron crystallography	11
Structural and functional characterization of a multi-domain GH92 α-1,2-mannosidase from Neobacillus novalis	11
Probabilistic single-particle cryo-EM ab initio 3D reconstruction in SIMPLE	11
Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin	11
Crystal structure of the monocupin ring-cleaving dioxygenase 5-nitrosalicylate 1,2-dioxygenase fromBradyrhizobiumsp.	11
The LH–DH module of bacterial replicative helicases is the common binding site for DciA and other helicase loaders	10
Raynals , an online tool for the analysis of dynamic light scattering	10
Native glycosylation and binding of the antidepressant paroxetine in a low-resolution crystal structure of human myeloperoxidase	10
Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects	10
Dependence of crystallographic atomic displacement parameters on temperature (25–150 K) for complexes of horse liver alcohol dehydrogenase	10
Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase	9
Restoration of the 3D structure of insect flight muscle from a rotationally averaged 2D X-ray diffraction pattern	9

Polyelectrolyte coating of cryo-EM grids improves lateral distribution and prevents aggregation of macromolecules	9
Accelerating crystal structure determination with iterative AlphaFold prediction	9
Protonation states of hen egg-white lysozyme observed using D/H contrast neutron crystallography	9
Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum	9
Correcting systematic errors in diffraction data with modern scaling algorithms	9
Buccaneer model building with neural network fragment selection	9
Glycoside hydrolase subfamily GH5_57 features a highly redesigned catalytic interface to process complex hetero-β-mannans	9
Errors in structural biology are not the exception	9
The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF	9
Tomo Live : an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows	9
Structural insights into choline-O-sulfatase reveal the molecular determinants for ligand binding	9
Structural basis for substrate recognition in the Phytolacca americana glycosyltransferase PaGT3	9
Drosophila melanogaster frataxin: protein crystal and predicted solution structure with identification of the iron-binding regions	8
XFEL structure of carbonic anhydrase II: a comparative study of XFEL, NMR, X-ray and neutron structures	8
Post-translational modifications in the Protein Data Bank	8
Mechanistic insight into O=O bond formation upon model-independent visualization of the coordination geometry and ligand composition of Mn4Ca cofactor in dark-adapted photosystem II structu	8
Structural features of chloroplast trigger factor determined at 2.6 Å resolution	8
The impact of molecular variants, crystallization conditions and the space group on ligand–protein complexes: a case study on bacterial phosphotriesterase	8
Protein–macrocycle polymorphism: crystal form IV of the Ralstonia solanacearum lectin–sulfonato-calix[8]arene complex	8
High-resolution structures of the bound effectors avadomide (CC-122) and iberdomide (CC-220) highlight advantages and limitations of the MsCI4 soaking system	8
Atomic model validation using the CCP-EM software suite	8
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	8
VitroJet: new features and case studies	8
Inhibition of Schistosoma mansoni carbonic anhydrase by the antiparasitic drug clorsulon: X-ray crystallographic and in vitro studies	7
Thermostable homologues of the periplasmic siderophore-binding protein CeuE from Geobacillus stearothermophilus and Parageobacillus thermoglucosidasius	7
AutoPX: a new software package to process X-ray diffraction data from biomacromolecular crystals	7
Using deep-learning predictions of inter-residue distances for model validation	7
Investigation of how gate residues in the main channel affect the catalytic activity of Scytalidium thermophilum catalase	7
Crystal structures of 40- and 71-substitution variants of hydroxynitrile lyase from rubber tree	7
Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals	7
Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography	7
Global fitting of multiple data frames from SEC–SAXS to investigate the structure of next-generation nanodiscs	7
Towards the standardized presentation and publication of small-angle scattering data from biomolecules in solution	7
Crystal structure of the middle and C-terminal domains of Hsp90α labeled with a coumarin derivative reveals a potential allosteric binding site as a drug target	7
The CCP4 suite: integrative software for macromolecular crystallography	7
Increasing the bulk of the 1TEL–target linker and retaining the 10×His tag in a 1TEL–CMG2-vWa construct improves crystal order and diffraction limits	7
The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study report. Corrigendum	7
Structural snapshot of a glycoside hydrolase family 8 endo-β-1,4-glucanase capturing the state after cleavage of the scissile bond	7
FLEXR: automated multi-conformer model building using electron-density map sampling	7
Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography	7
Efficient high-resolution refinement in cryo-EM with stochastic gradient descent	6
Off-target structural insights: ArnA and AcrB in bacterial membrane-protein cryo-EM analysis	6
xia2.multiplex: a multi-crystal data-analysis pipeline	6
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	6
Conformational transition of the Ixodes ricinus salivary serpin Iripin-4	6
SCOMAP-XD: atomistic deuterium contrast matching for small-angle neutron scattering in biology	6
Analysis of crystallographic phase retrieval using iterative projection algorithms	6
Racemic crystal structures of A-DNA duplexes	6
Neutron crystallographic refinement with REFMAC5 from the CCP4 suite	6
Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM	6
Identification and characterization of two drug-like fragments that bind to the same cryptic binding pocket of Burkholderia pseudomallei DsbA	6
Crystal structure of the putative cell-wall lipoglycan biosynthesis protein LmcA from Mycobacterium smegmatis	6
Jan Drenth (1925–2025)	6
CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures	6
MrParse : finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more	6
Databases for intrinsically disordered proteins	6
Substrate-induced dimerization of elaiophylin glycosyltransferase reveals a novel self-activating form of glycosyltransferase for symmetric glycosylation	6
Unravelling the regulation pathway of photosynthetic AB-GAPDH	6
Structure-based discovery of an antipsychotic drug, paliperidone, as a modulator of human superoxide dismutase 1: a potential therapeutic target in amyotrophic lateral sclerosis	6
A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography	6
30 years of Acta D	5
Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography	5
Direct calculation of cryo-EM and crystallographic model maps for real-space refinement	5
High-confidence placement of low-occupancy fragments into electron density using the anomalous signal of sulfur and halogen atoms	5
Structural and functional characterization of a thermostable secretory phospholipase A2 from Sciscionella marina and its application in liposome biotransformation	5
Crystal structure of a novel homodimericD-allulose 3-epimerase from a Clostridia bacterium	5
Structural and functional investigation of the human snRNP assembly factor AAR2 in complex with the RNase H-like domain of PRPF8	5
Improving macromolecular structure refinement with metal-coordination restraints	5
Two states of a light-sensitive membrane protein captured at room temperature using thin-film sample mounts	5
HEIDI: an experiment-management platform enabling high-throughput fragment and compound screening	5
The structure and molecular dynamics of prolyl oligopeptidase from Microbulbifer arenaceous provide insights into catalytic and regulatory mechanisms	5
CryoLike : a Python package for cryo-electron microscopy image-to-structure likelihood calculations	5
Perspective on structure predictions of disorder	5
Module walking using an SH3-like cell-wall-binding domain leads to a new GH184 family of muramidases	5
Photosystem II: light-dependent oscillation of ligand composition at its active site	5
Kinetic and structural studies of the reaction of Escherichia coli dihydrodipicolinate synthase with (S)-2-bromopropionate	5
Structure of reverse gyrase with a minimal latch that supports ATP-dependent positive supercoiling without specific interactions with the topoisomerase domain	5
Introduction to the virtual thematic issue on room-temperature biological crystallography	5
Novel starting points for fragment-based drug design against mycobacterial thioredoxin reductase identified using crystallographic fragment screening	5
From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons	5

The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1	5
Using cryo-EM to understand the assembly pathway of respiratory complex I	4
Correction of rhodopsin serial crystallography diffraction intensities for a lattice-translocation defect	4
Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution	4
A snapshot love story: what serial crystallography has done and will do for us	4
Useful experimental aspects of small-wedge synchrotron crystallography for accurate structure analysis of protein molecules	4
Native SAD phasing at room temperature	4
Determining the oxidation state of elements by X-ray crystallography	4
Crystal structure of dihydrofolate reductase from the emerging pathogenic fungus Candida auris	4
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER	4
AlphaFold-guided molecular replacement for solving challenging crystal structures	4
Structural insight into an anti-BRIL Fab as a G-protein-coupled receptor crystallization chaperone	4
Protonation of histidine rings using quantum-mechanical methods	4
A case for glycerol as an acceptable additive for single-particle cryoEM samples	4
Characterization of novel mevalonate kinases from the tardigrade Ramazzottius varieornatus and the psychrophilic archaeon Methanococcoides burtonii	4
Crystal structure of glycerol kinase from Trypanosoma cruzi, a potential molecular target in Chagas disease	4
Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible subs	4
Structural and functional characterization of the novel endo-α(1,4)-fucoidanase Mef1 from the marine bacterium Muricauda eckloniae	4
Crystal structure of a polyglycine hydrolase determined using a RoseTTAFold model	4
CCP4 Cloud for structure determination and project management in macromolecular crystallography	4
What shapes template-matching performance in cryogenic electron tomography in situ?	4
Enhanced capabilities for multi-crystal data collection based on double mesh scans	3
Structure–function studies of a novel laccase-like multicopper oxidase fromThermothelomyces thermophilaprovide insights into its biological role	3
EMinsight : a tool to capture cryoEM microscope configuration and experimental outcomes for analysis and deposition	3
Perspective on a large-scale ligand structure characterization	3
Current trends in macromolecular model refinement and validation	3
Likelihood-based docking of models into cryo-EM maps	3
Rhizobium etli has two L-asparaginases with low sequence identity but similar structure and catalytic center	3
Room-temperature serial synchrotron crystallography of Drosophila cryptochrome	3
Structural basis of ligand recognition and transport by Sfh2, a yeast phosphatidylinositol transfer protein of the Sec14 superfamily	3
The ManifoldEM method for cryo-EM: a step-by-step breakdown accompanied by a modern Python implementation	3
Structure of the plant growth-promoting factor YxaL from the rhizobacterium Bacillus velezensis and its application to protein engineering	3
Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6	3
Factors affecting macromolecule orientations in thin films formed in cryo-EM	3
Structure of a hydrophobic leucinostatin derivative determined by host lattice display	3
The parallel-stranded d(CGA) duplex is a highly predictable structural motif with two conformationally distinct strands	3
The crystal structure of mycothiol disulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria	3
Validation of electron-microscopy maps using solution small-angle X-ray scattering	3
Crystal-packing analysis of translation initiation factor 2 reveals new details of its function	3
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	3
Robust and automatic beamstop shadow outlier rejection: combining crystallographic statistics with modern clustering under a semi-supervised learning strategy	3
Time-Resolved Methods in Structural Biology, Methods in Enzymology Volume 709. Edited by Peter Moody and Hanna Kwon. Academic Press, New York, 2024, pp. 412. ISBN-10 044331456X, ISBN-13 978-044	3
Q -score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps	3
Reconstructing biological molecules with help from video gamers	3
Application of sulfur SAD to small crystals with a large asymmetric unit and anomalous substructure	3
Structural dynamics of IDR interactions in human SFPQ and implications for liquid–liquid phase separation	3