Acta Crystallographica Section D-Structural Biology

Article	Citations
Comparison of two crystal polymorphs of NowGFP reveals a new conformational state trapped by crystal packing	866
Crystallographic fragment screening against SARS-CoV-2 nonstructural protein 1 using the F2X-Entry Screen and a newly developed fragment library	83
Structure of the Fab fragment of a humanized 5E5 antibody to a cancer-specific Tn-MUC1 epitope	65
Cryo-EM single-particle analysis expanding towards increasingly native samples	64
Limiting the effects of radiation damage in MicroED through dose selection during data processing	57
Using graphlet degree vectors to predict atomic displacement parameters in protein structures	55
Completion of partial structures using Patterson maps with the CrysFormer machine-learning model	51
EMhub: a web platform for data management and on-the-fly processing in scientific facilities	42
Structural flexibility of Toscana virus nucleoprotein in the presence of a single-chain camelid antibody	39
Structures of α-galactosaminidases from the CAZy GH114 family and homologs defining a new GH191 family of glycosidases	34
Structural characterization of the ACDC domain from ApiAP2 proteins, a potential molecular target against apicomplexan parasites	32
Data collection from crystals grown in microfluidic droplets	30
Structures of permuted halves of a modern ribose-binding protein	24
Structural studies of NAD + -dependent methanol dehydrogenase 1 from Bacillus methanolicus MGA3	23
Critical evaluation of three cryo-EM structures of particulate methane monooxygenase by quantum refinement	23
Identifying and avoiding radiation damage in macromolecular crystallography	23
The crystal structure of CbpD clarifies substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases	21
Crystal structure of DNA polymerase I from Thermus phage G20c	20
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	20
Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals	20
An alternative conformation of the N-terminal loop of human dihydroorotate dehydrogenase drives binding to a potent antiproliferative agent	19
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)	19
A cryo-EM processing pipeline for microtubules using CryoSPARC	19
Validation of helical symmetry parameters in the EMDB	19
Training undergraduate research assistants with an outcome-oriented and skill-based mentoring strategy	18

Overall protein structure quality assessment using hydrogen-bonding parameters	18
Statistical analyses of the oxidized P-clusters in MoFe proteins using the bond-valence method: towards their electron transfer in nitrogenases	18
Analysis and validation of overall N-glycan conformation in Privateer	18
Structural studies of β-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus	17
Medical contrast agents as promising tools for biomacromolecular SAXS experiments	16
Crystal structure of coagulation factor XII N-terminal domains 1–5	16
Radiation damage in sub-Ångström resolution macromolecular crystallography: a low-dose study	15
A high-resolution data set of fatty acid-binding protein structures. III. Unexpectedly high occurrence of wrong ligands	15
Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned	15
Structural study of Nicotiana benthamiana NADPH-dependent thioredoxin reductase C and its molecular mechanism of interaction with 2-Cys peroxiredoxin	14
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.	14
Deciphering the crystal structure of a novel nanobody against the NEIL1 DNA glycosylase	14
Pillar data-acquisition strategies for cryo-electron tomography of beam-sensitive biological samples	14
Michael James (1940–2023)	14
Alexei Vagin (1944–2023)	14
3D structures of the Plasmodium vivax subtilisin-like drug target SUB1 reveal conformational changes to accommodate a substrate-derived α-ketoamide inhibitor	14
Preparation and characterization of inactivated tick-borne encephalitis virus samples for single-particle imaging at the European XFEL	13
Crystal structures of the molecular class A β-lactamase TEM-171 and its complexes with tazobactam	13
The T2 structure of polycrystalline cubic human insulin	12
Probabilistic single-particle cryo-EM ab initio 3D reconstruction in SIMPLE	12
Direct phasing algorithm for protein crystals with high solvent content using low-resolution diffraction data	12
Biochemical and structural insights into an unusual, alkali-metal-independent S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803	12
Crystal structure of the monocupin ring-cleaving dioxygenase 5-nitrosalicylate 1,2-dioxygenase fromBradyrhizobiumsp.	12
Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket	12
Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks	12
Raynals , an online tool for the analysis of dynamic light scattering	11
Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects	11
Glycoside hydrolase subfamily GH5_57 features a highly redesigned catalytic interface to process complex hetero-β-mannans	11
Dependence of crystallographic atomic displacement parameters on temperature (25–150 K) for complexes of horse liver alcohol dehydrogenase	11
Elucidating polymorphs of crystal structures by intensity-based hierarchical clustering analysis of multiple diffraction data sets	11
Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy	11
Structural mechanism of Escherichia coli cyanase	11
Breaking barriers: transitioning from X-ray crystallography to cryo-EM for structural studies	11
Structural and functional characterization of a multi-domain GH92 α-1,2-mannosidase from Neobacillus novalis	11
Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin	11
Accelerating crystal structure determination with iterative AlphaFold prediction	11
Native glycosylation and binding of the antidepressant paroxetine in a low-resolution crystal structure of human myeloperoxidase	11
Structures of variants of Escherichia coli flavodiiron-type nitric oxide reductase reveal changes in the di-iron site	11
The LH–DH module of bacterial replicative helicases is the common binding site for DciA and other helicase loaders	11
Cryo-EM structure of ALC1 in an open conformation bound to a PARylated nucleosome	10
Alphafuser : a parsimonious approach to predicting higher-order protein complexes	10
A short story of the long road to cryo-EM in Portugal	10
Restoration of the 3D structure of insect flight muscle from a rotationally averaged 2D X-ray diffraction pattern	9
Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase	9
Tomo Live : an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows	9
Buccaneer model building with neural network fragment selection	9
Errors in structural biology are not the exception	9
Correcting systematic errors in diffraction data with modern scaling algorithms	9
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	9
Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum	9

The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF	9
Polyelectrolyte coating of cryo-EM grids improves lateral distribution and prevents aggregation of macromolecules	9
VitroJet: new features and case studies	9
Coupled on-line in crystallo UV–Vis absorption spectroscopy and X-ray crystallography to compare specific radiation damage in metal-containing proteins a	8
Protein–macrocycle polymorphism: crystal form IV of the Ralstonia solanacearum lectin–sulfonato-calix[8]arene complex	8
Strategies for mitigating radiation damage and improving data completeness in 3D electron diffraction of protein crystals	8
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	8
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	8
Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography	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
XFEL structure of carbonic anhydrase II: a comparative study of XFEL, NMR, X-ray and neutron structures	8
Drosophila melanogaster frataxin: protein crystal and predicted solution structure with identification of the iron-binding regions	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
Phosphatidylinositol transfer protein α binds microcolins in its open conformation	8
Post-translational modifications in the Protein Data Bank	8
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	8
Towards the standardized presentation and publication of small-angle scattering data from biomolecules in solution	7
AutoPX: a new software package to process X-ray diffraction data from biomacromolecular crystals	7
Crystal structure of Schistosoma mansoni cathepsin D1 in complex with a nanobody reveals the conformation of the propeptide-bound state	7
The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study re	7
Conformational transition of the Ixodes ricinus salivary serpin Iripin-4	7
Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals	7
Automated workflows for strategy computation and data collection at synchrotron beamlines	7
Using deep-learning predictions of inter-residue distances for model validation	7
Crystal structures of 40- and 71-substitution variants of hydroxynitrile lyase from rubber tree	7
The CCP4 suite: integrative software for macromolecular crystallography	7
Thermostable homologues of the periplasmic siderophore-binding protein CeuE from Geobacillus stearothermophilus and Parageobacillus thermoglucosidasius	7
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
FLEXR: automated multi-conformer model building using electron-density map sampling	6
Investigation of how gate residues in the main channel affect the catalytic activity of Scytalidium thermophilum catalase	6
Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography	6
Bayesian perspective for orientation determination in cryo-EM with application to structural heterogeneity analysis	6
The human TIMP-1 unbound structure provides a platform for fragment screening	6
Jan Drenth (1925–2025)	6
Associating protein residues in the literature with structural data	6
Analysis of crystallographic phase retrieval using iterative projection algorithms	5
Efficient high-resolution refinement in cryo-EM with stochastic gradient descent	5
Structure of reverse gyrase with a minimal latch that supports ATP-dependent positive supercoiling without specific interactions with the topoisomerase domain	5
30 years of Acta D	5
Quantifying distributions of cryo-EM projections	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	5
Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM	5
Neutron crystallographic refinement with REFMAC5 from the CCP4 suite	5
HEIDI: an experiment-management platform enabling high-throughput fragment and compound screening	5
High-confidence placement of low-occupancy fragments into electron density using the anomalous signal of sulfur and halogen atoms	5
Photosystem II: light-dependent oscillation of ligand composition at its active site	5
A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography	5
SCOMAP-XD: atomistic deuterium contrast matching for small-angle neutron scattering in biology	5
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	5
Off-target structural insights: ArnA and AcrB in bacterial membrane-protein cryo-EM analysis	5
Kinetic and structural studies of the reaction of Escherichia coli dihydrodipicolinate synthase with (S)-2-bromopropionate	5
Improving macromolecular structure refinement with metal-coordination restraints	5
Direct calculation of cryo-EM and crystallographic model maps for real-space refinement	5
Crystal structures of Fsc1, a novel autophagy factor that mediates autophagosome–vacuole fusion in fission yeast	5
Introduction to the virtual thematic issue on room-temperature biological crystallography	4
SASBDB reaches 5000 data sets: empowering open science and next-generation SAS analysis	4
The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1	4
CryoLike : a Python package for cryo-electron microscopy image-to-structure likelihood calculations	4
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER	4
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	4
Native SAD phasing at room temperature	4
Perspective on structure predictions of disorder	4
Module walking using an SH3-like cell-wall-binding domain leads to a new GH184 family of muramidases	4
Crystal structure of a novel homodimericD-allulose 3-epimerase from a Clostridia bacterium	4
Novel starting points for fragment-based drug design against mycobacterial thioredoxin reductase identified using crystallographic fragment screening	4
Optimal 1TEL–target protein linker character is target protein-dependent	4
Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution	4
Correction of rhodopsin serial crystallography diffraction intensities for a lattice-translocation defect	4
Crystal structure of glycerol kinase from Trypanosoma cruzi, a potential molecular target in Chagas disease	4
From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons	4
Definition of the catalytic cleft and product profile of a GH5_5 cellulase from Thermoascus aurantiacus	4
Structural and functional investigation of the human snRNP assembly factor AAR2 in complex with the RNase H-like domain of PRPF8	4
Structural and functional characterization of the novel endo-α(1,4)-fucoidanase Mef1 from the marine bacterium Muricauda eckloniae	4
Structural and functional characterization of a thermostable secretory phospholipase A2 from Sciscionella marina and its application in liposome biotransformation	4
Characterization of novel mevalonate kinases from the tardigrade Ramazzottius varieornatus and the psychrophilic archaeon Methanococcoides burtonii	4
Crystal structure of a polyglycine hydrolase determined using a RoseTTAFold model	4
Validation of electron-microscopy maps using solution small-angle X-ray scattering	3
Updating direct methods V. Phasing when triplet invariants are estimated via the Patterson map	3

Radiation-induced peroxide rupture and its temperature-dependent repair probed by homogeneous X-ray irradiation	3
CCP4 Cloud for structure determination and project management in macromolecular crystallography	3
Useful experimental aspects of small-wedge synchrotron crystallography for accurate structure analysis of protein molecules	3
Crystal structure of dihydrofolate reductase from the emerging pathogenic fungus Candida auris	3
Reconstructing biological molecules with help from video gamers	3
What shapes template-matching performance in cryogenic electron tomography in situ?	3
Decision-making in serial crystallography: a simple test to quickly determine whether sufficient data have been collected	3
A snapshot love story: what serial crystallography has done and will do for us	3
Protonation of histidine rings using quantum-mechanical methods	3
Using cryo-EM to understand the assembly pathway of respiratory complex I	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
Q -score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps	3
Rational acquisition of laboratory equipment: an accurate mathematical model to estimate the trade-offs in shared and nonshared equipment	3
Damage-limited resolution for X-ray and electron microscopy of organic specimens	3
AlphaFold -guided molecular replacement for solving challenging crystal structures	3
Reminiscences of Phil Bourne (1953–2026) and the IUCr	3
Structural insight into an anti-BRIL Fab as a G-protein-coupled receptor crystallization chaperone	3
Application of sulfur SAD to small crystals with a large asymmetric unit and anomalous substructure	3
Crystal-packing analysis of translation initiation factor 2 reveals new details of its function	2
Cryo-EM reveals ArnA contamination during purification of a ciliary protein complex	2
Room-temperature serial synchrotron crystallography of Drosophila cryptochrome	2
EMinsight : a tool to capture cryoEM microscope configuration and experimental outcomes for analysis and deposition	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 044331456X, ISBN-13 978-044	2
Structure of a hydrophobic leucinostatin derivative determined by host lattice display	2
Room-temperature X-ray data collection enabled the structural determination of statin-bound CYP105A1	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
Structural analysis of LpqY, a substrate-binding protein from the SugABC transporter of Mycobacterium tuberculosis, provides insights into its trehalose specificity	2
Expansion of the diversity of dispersin scaffolds	2
The evolving role of structural biology in pharma: integration of X-ray crystallography, cryo-electron microscopy and beyond	2
Cryo-EM structure of adeno-associated virus 4 at 2.2 Å resolution	2
Structure–function studies of a novel laccase-like multicopper oxidase fromThermothelomyces thermophilaprovide insights into its biological role	2
The crystal structure of EpHTT, a hydroxycinnamoyl transferase from Echinacea purpurea	2
Robust and automatic beamstop shadow outlier rejection: combining crystallographic statistics with modern clustering under a semi-supervised learning strategy	2
Enhanced capabilities for multi-crystal data collection based on double mesh scans	2
The crystal structure of mycothiol disulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria	2
The ManifoldEM method for cryo-EM: a step-by-step breakdown accompanied by a modern Python implementation	2
Perspective on a large-scale ligand structure characterization	2
Continuous development in macromolecular crystallography with CCP4	2
Welcoming two new Co-editors	2
Polo-like kinase 1–inhibitor co-complex structures via the surface-entropy reduction approach and a DARPin-assisted approach	2
Likelihood-based signal and noise analysis for docking of models into cryo-EM maps	2
Structural basis for high-affinity inhibitor binding to lipid kinases PIP4K2A and PIP4K2B	2
Structural basis of ligand recognition and transport by Sfh2, a yeast phosphatidylinositol transfer protein of the Sec14 superfamily	2
Structural dynamics of IDR interactions in human SFPQ and implications for liquid–liquid phase separation	2
Current trends in macromolecular model refinement and validation	2
Factors affecting macromolecule orientations in thin films formed in cryo-EM	2
Structure and stability of an apo thermophilic esterase that hydrolyzes polyhydroxybutyrate	2
The crystal structure of an uncharacterized domain of P113 from Plasmodium falciparum	2
Wolfram Saenger (1939–2026)	2
Duplicate entries in the Protein Data Bank: how to detect and handle them	2