Acta Crystallographica Section D-Structural Biology

Article	Citations
Completion of partial structures using Patterson maps with the CrysFormer machine-learning model	933
Cryo-EM single-particle analysis expanding towards increasingly native samples	91
Using graphlet degree vectors to predict atomic displacement parameters in protein structures	73
Structure of the Fab fragment of a humanized 5E5 antibody to a cancer-specific Tn-MUC1 epitope	68
EMhub: a web platform for data management and on-the-fly processing in scientific facilities	57
Comparison of two crystal polymorphs of NowGFP reveals a new conformational state trapped by crystal packing	54
Limiting the effects of radiation damage in MicroED through dose selection during data processing	47
Crystallographic fragment screening against SARS-CoV-2 nonstructural protein 1 using the F2X-Entry Screen and a newly developed fragment library	40
Scotty : lattice coincidences in the Protein Data Bank	36
PETIMOT : a novel framework for inferring protein motions from sparse data using SE(3)-equivariant graph neural networks	36
Structural flexibility of Toscana virus nucleoprotein in the presence of a single-chain camelid antibody	31
Structures of α-galactosaminidases from the CAZy GH114 family and homologs defining a new GH191 family of glycosidases	30
Structural studies of NAD + -dependent methanol dehydrogenase 1 from Bacillus methanolicus MGA3	23
Identifying and avoiding radiation damage in macromolecular crystallography	23
Critical evaluation of three cryo-EM structures of particulate methane monooxygenase by quantum refinement	22
Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals	21
Crystal structure of DNA polymerase I from Thermus phage G20c	21
Structures of permuted halves of a modern ribose-binding protein	20
Structural characterization of the ACDC domain from ApiAP2 proteins, a potential molecular target against apicomplexan parasites	20
Interactive segmentation of membrane and membrane-mimic densities in cryo-EM maps	20
Biochemical and structural characterization of a tail-spike protein with depolymerase activity identified in a marine podovirus	20
Analysis and validation of overall N -glycan conformation in Privateer	19
Optimal 1TEL–target protein linker character is target protein-dependent. Corrigendum	19
An alternative conformation of the N-terminal loop of human dihydroorotate dehydrogenase drives binding to a potent antiproliferative agent	18
A cryo-EM processing pipeline for microtubules using CryoSPARC	18

Validation of helical symmetry parameters in the EMDB	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	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)	17
Overall protein structure quality assessment using hydrogen-bonding parameters	16
Experimental estimation of copper-site geometry reproducibility in biologically relevant redox and saccharide-bound states of a model lytic polysaccharide monooxygenase	16
Structure of the Arabidopsis receptor kinase SRF6 ectodomain determined from crystals obtained using the LRR crystallization screen	15
Structural basis for the fast maturation of pcStar, a photoconvertible fluorescent protein. Erratum	15
Miroslav Z. Papiz (1955–2026)	15
Structural basis for a p21-activated kinase 4 and nicotinamide phosphoribosyltransferase dual inhibitor	15
Structural studies of β-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus	14
Crystal structure of coagulation factor XII N-terminal domains 1–5	14
Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned	14
Radiation damage in sub-Ångström resolution macromolecular crystallography: a low-dose study	13
Deciphering the crystal structure of a novel nanobody against the NEIL1 DNA glycosylase	13
A high-resolution data set of fatty acid-binding protein structures. III. Unexpectedly high occurrence of wrong ligands	13
3D structures of the Plasmodium vivax subtilisin-like drug target SUB1 reveal conformational changes to accommodate a substrate-derived α-ketoamide inhib	13
Statistical analyses of the oxidized P-clusters in MoFe proteins using the bond-valence method: towards their electron transfer in nitrogenases	13
Medical contrast agents as promising tools for biomacromolecular SAXS experiments	13
The T 2 structure of polycrystalline cubic human insulin	12
Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket	12
Pillar data-acquisition strategies for cryo-electron tomography of beam-sensitive biological samples	12
Alexei Vagin (1944–2023)	12
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.	12
Michael James (1940–2023)	12
Structural study of Nicotiana benthamiana NADPH-dependent thioredoxin reductase C and its molecular mechanism of interaction with 2-Cys peroxiredoxin	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
Structures of variants of Escherichia coli flavodiiron-type nitric oxide reductase reveal changes in the di-iron site	11
Crystal structure of the monocupin ring-cleaving dioxygenase 5-nitrosalicylate 1,2-dioxygenase from Bradyrhizobium sp.	11
Raynals , an online tool for the analysis of dynamic light scattering	11
Preparation and characterization of inactivated tick-borne encephalitis virus samples for single-particle imaging at the European XFEL	11
Direct phasing algorithm for protein crystals with high solvent content using low-resolution diffraction data	11
Elucidating polymorphs of crystal structures by intensity-based hierarchical clustering analysis of multiple diffraction data sets	11
The LH–DH module of bacterial replicative helicases is the common binding site for DciA and other helicase loaders	11
Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin	10
Dose-dependent structural and electron-density features in the lytic polysaccharide monooxygenase Nc AA9D	10
Structural mechanism of Escherichia coli cyanase	10
Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy	10
Glycoside hydrolase subfamily GH5_57 features a highly redesigned catalytic interface to process complex hetero-β-mannans	9
Native glycosylation and binding of the antidepressant paroxetine in a low-resolution crystal structure of human myeloperoxidase	9
Buccaneer model building with neural network fragment selection	9
Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects	9
A short story of the long road to cryo-EM in Portugal	9
Breaking barriers: transitioning from X-ray crystallography to cryo-EM for structural studies	9
The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF	9
Cryo-EM structure of ALC1 in an open conformation bound to a PARylated nucleosome	9
Alphafuser : a parsimonious approach to predicting higher-order protein complexes	9
Accelerating crystal structure determination with iterative AlphaFold prediction	9
Dependence of crystallographic atomic displacement parameters on temperature (25–150 K) for complexes of horse liver alcohol dehydrogenase	9
Atypical homodimerization revealed by the structure of the ( S )-enantioselective haloalkane dehalogenase DmmarA from Mycobacteriu	8

Errors in structural biology are not the exception	8
Polyelectrolyte coating of cryo-EM grids improves lateral distribution and prevents aggregation of macromolecules	8
Correcting systematic errors in diffraction data with modern scaling algorithms	8
VitroJet: new features and case studies	8
Restoration of the 3D structure of insect flight muscle from a rotationally averaged 2D X-ray diffraction pattern	8
Simulating neutron protein crystallography experiments: applications to the development of the NMX instrument at ESS	8
Tomo Live : an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows	8
Strategies for mitigating radiation damage and improving data completeness in 3D electron diffraction of protein crystals	7
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.	7
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	7
The impact of molecular variants, crystallization conditions and the space group on ligand–protein complexes: a case study on bacterial phosphotriesterase	7
Mechanistic insight into O=O bond formation upon model-independent visualization of the coordination geometry and ligand composition of Mn 4 Ca cofac	7
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	7
Phosphatidylinositol transfer protein α binds microcolins in its open conformation	7
Drosophila melanogaster frataxin: protein crystal and predicted solution structure with identification of the iron-binding regions	7
Coupled on-line in crystallo UV–Vis absorption spectroscopy and X-ray crystallography to compare specific radiation damage in metal-containing proteins a	7
Protein–macrocycle polymorphism: crystal form IV of the Ralstonia solanacearum lectin–sulfonato-calix[8]arene complex	7
An unattended image-processing pipeline for on-the-fly quality assessment and 3D exploration in cryo-EM	7
Structural features of chloroplast trigger factor determined at 2.6 Å resolution	6
Thermostable homologues of the periplasmic siderophore-binding protein CeuE from Geobacillus stearothermophilus and Parageobacillu	6
Using deep-learning predictions of inter-residue distances for model validation	6
Crystal structure of Schistosoma mansoni cathepsin D1 in complex with a nanobody reveals the conformation of the propeptide-bound state	6
XFEL structure of carbonic anhydrase II: a comparative study of XFEL, NMR, X-ray and neutron structures	6
Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography	6
Automated workflows for strategy computation and data collection at synchrotron beamlines	6
Crystal structures of 40- and 71-substitution variants of hydroxynitrile lyase from rubber tree	6
Post-translational modifications in the Protein Data Bank	6
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	6
The CCP 4 suite: integrative software for macromolecular crystallography	6
The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study re	6
Structural basis of regioselective double halogenation of the β-carboline tryptoline by the single-component halogenase AetF	5
Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM	5
Conformational transition of the Ixodes ricinus salivary serpin Iripin-4	5
FLEXR : automated multi-conformer model building using electron-density map sampling	5
Bayesian perspective for orientation determination in cryo-EM with application to structural heterogeneity analysis	5
Efficient high-resolution refinement in cryo-EM with stochastic gradient descent	5
Off-target structural insights: ArnA and AcrB in bacterial membrane-protein cryo-EM analysis	5
The human TIMP-1 unbound structure provides a platform for fragment screening	5
Towards the standardized presentation and publication of small-angle scattering data from biomolecules in solution	5
Unravelling the regulation pathway of photosynthetic AB-GAPDH	5
A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography	5
Analysis of crystallographic phase retrieval using iterative projection algorithms	5
Associating protein residues in the literature with structural data	5
Substrate-induced dimerization of elaiophylin glycosyltransferase reveals a novel self-activating form of glycosyltransferase for symmetric glycosylation	5
Investigation of how gate residues in the main channel affect the catalytic activity of Scytalidium thermophilum catalase	5
Structure-based discovery of an antipsychotic drug, paliperidone, as a modulator of human superoxide dismutase 1: a potential therapeutic target in amyotrophic lateral sclerosis	4
Neutron crystallographic refinement with REFMAC 5 from the CCP 4 suite	4
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	4
Structure of reverse gyrase with a minimal latch that supports ATP-dependent positive supercoiling without specific interactions with the topoisomerase domain	4
Module walking using an SH3-like cell-wall-binding domain leads to a new GH184 family of muramidases	4
Optimal 1TEL–target protein linker character is target protein-dependent	4
The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1	4
Direct calculation of cryo-EM and crystallographic model maps for real-space refinement	4
Photosystem II: light-dependent oscillation of ligand composition at its active site	4
Jan Drenth (1925–2025)	4
Crystal structures of Fsc1, a novel autophagy factor that mediates autophagosome–vacuole fusion in fission yeast	4
HEIDI: an experiment-management platform enabling high-throughput fragment and compound screening	4
High-confidence placement of low-occupancy fragments into electron density using the anomalous signal of sulfur and halogen atoms	4
From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons	4
CryoLike : a Python package for cryo-electron microscopy image-to-structure likelihood calculations	4
SASBDB reaches 5000 data sets: empowering open science and next-generation SAS analysis	4
Improving macromolecular structure refinement with metal-coordination restraints	4
Definition of the catalytic cleft and product profile of a GH5_5 cellulase from Thermoascus aurantiacus	4
SCOMAP-XD : atomistic deuterium contrast matching for small-angle neutron scattering in biology	4
30 years of Acta D	4
Crystal structure of a novel homodimeric D -allulose 3-epimerase from a Clostridia bacterium	4
Crystal structure of pilus-specific sortase from Enterococcus faecalis reveals both open and closed conformations: insights into loop dynamics and substr	4
Introduction to the virtual thematic issue on room-temperature biological crystallography	4
Structural and functional investigation of the human snRNP assembly factor AAR2 in complex with the RNase H-like domain of PRPF8	4
Novel starting points for fragment-based drug design against mycobacterial thioredoxin reductase identified using crystallographic fragment screening	4
Quantifying distributions of cryo-EM projections	4
Crystal structure of dihydrofolate reductase from the emerging pathogenic fungus Candida auris	3
Structural and functional characterization of a thermostable secretory phospholipase A 2 from Sciscionella marina	3
Crystal structure of glycerol kinase from Trypanosoma cruzi , a potential molecular target in Chagas disease	3
Using cryo-EM to understand the assembly pathway of respiratory complex I	3
Protonation of histidine rings using quantum-mechanical methods	3
LowDoseWizard : rapid and standardized setup of low-dose cryo-TEM imaging in SerialEM	3
Useful experimental aspects of small-wedge synchrotron crystallography for accurate structure analysis of protein molecules	3
It started off as a Cys, how did it end up like this? Identifying the extent of unmodelled oxidatively modified cysteines within the Protein Data Bank	3
Perspective on structure predictions of disorder	3

A snapshot love story: what serial crystallography has done and will do for us	3
Correction of rhodopsin serial crystallography diffraction intensities for a lattice-translocation defect	3
CCP 4 Cloud for structure determination and project management in macromolecular crystallography	3
Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution	3
Structural and functional characterization of the novel endo-α(1,4)-fucoidanase Mef1 from the marine bacterium Muricauda eckloniae	3
Structural insight into an anti-BRIL Fab as a G-protein-coupled receptor crystallization chaperone	3
Rational acquisition of laboratory equipment: an accurate mathematical model to estimate the trade-offs in shared and nonshared equipment	3
Characterization of novel mevalonate kinases from the tardigrade Ramazzottius varieornatus and the psychrophilic archaeon Methanoc	3
Reminiscences of Phil Bourne (1953–2026) and the IUCr	3
Crystal structure of a polyglycine hydrolase determined using a RoseTTAFold model	2
Updating direct methods VI. The extended use of the information contained in the Patterson map	2
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	2
Damage-limited resolution for X-ray and electron microscopy of organic specimens	2
The crystal structure of EpHTT, a hydroxycinnamoyl transferase from Echinacea purpurea	2
Structure of a hydrophobic leucinostatin derivative determined by host lattice display	2
Replacement soaking for human tankyrase 2 enables studies on substrate analogues and inhibitors	2
Duplicate entries in the Protein Data Bank: how to detect and handle them	2
Validation of electron-microscopy maps using solution small-angle X-ray scattering	2
Structural basis for high-affinity inhibitor binding to lipid kinases PIP4K2A and PIP4K2B	2
What shapes template-matching performance in cryogenic electron tomography in situ?	2
Likelihood-based docking of models into cryo-EM maps	2
Robust and automatic beamstop shadow outlier rejection: combining crystallographic statistics with modern clustering under a semi-supervised learning strategy	2
AlphaFold -guided molecular replacement for solving challenging crystal structures	2
Structure and stability of an apo thermophilic esterase that hydrolyzes polyhydroxybutyrate	2
Structural dynamics of IDR interactions in human SFPQ and implications for liquid–liquid phase separation	2
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 0443314	2
Cryo-EM reveals ArnA contamination during purification of a ciliary protein complex	2
Current trends in macromolecular model refinement and validation	2
Wolfram Saenger (1939–2026)	2
The ManifoldEM method for cryo-EM: a step-by-step breakdown accompanied by a modern Python implementation	2
Rhizobium etli has two L -asparaginases with low sequence identity but similar structure and catalytic center	2
Perspective on a large-scale ligand structure characterization	2
Q -score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps	2
The crystal structure of mycothiol disulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria	2
Likelihood-based signal and noise analysis for docking of models into cryo-EM maps	2
Structure–function studies of a novel laccase-like multicopper oxidase from Thermothelomyces thermophila provide insights into its biological role	2
Radiation-induced peroxide rupture and its temperature-dependent repair probed by homogeneous X-ray irradiation	2
Enhanced capabilities for multi-crystal data collection based on double mesh scans	2
Reconstructing biological molecules with help from video gamers	2
Cryo-EM structure of adeno-associated virus 4 at 2.2 Å resolution	2
Factors affecting macromolecule orientations in thin films formed in cryo-EM	2
The evolving role of structural biology in pharma: integration of X-ray crystallography, cryo-electron microscopy and beyond	2
Crystal-packing analysis of translation initiation factor 2 reveals new details of its function	2
Decision-making in serial crystallography: a simple test to quickly determine whether sufficient data have been collected	2
EMinsight : a tool to capture cryoEM microscope configuration and experimental outcomes for analysis and deposition	2
Updating direct methods V. Phasing when triplet invariants are estimated via the Patterson map	2
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER	2
Room-temperature X-ray data collection enabled the structural determination of statin-bound CYP105A1	2