Acta Crystallographica Section D-Structural Biology

Article	Citations
Cryo-EM single-particle structure refinement and map calculation usingServalcat	108
Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling	106
The CCP4 suite: integrative software for macromolecular crystallography	101
Implications of AlphaFold2 for crystallographic phasing by molecular replacement	62
Crystal structures of the selenoprotein glutathione peroxidase 4 in its apo form and in complex with the covalently bound inhibitor ML162	56
Two particle-picking procedures for filamentous proteins: SPHIRE-crYOLO filament mode and SPHIRE-STRIPER	45
Using photocaging for fast time-resolved structural biology studies	38
Combining high throughput and high quality for cryo-electron microscopy data collection	36
Protein structure prediction by AlphaFold2: are attention and symmetries all you need?	32
Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE	30
Through-grid wicking enables high-speed cryoEM specimen preparation	30
Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM	29
TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows	28
Density modification of cryo-EM maps	26
FragMAX: the fragment-screening platform at the MAX IV Laboratory	25
Structure of the N-terminal domain of ClpC1 in complex with the antituberculosis natural product ecumicin reveals unique binding interactions	24
xia2.multiplex: a multi-crystal data-analysis pipeline	24
eSPC: an online data-analysis platform for molecular biophysics	23
The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study report	23
Sample deposition onto cryo-EM grids: from sprays to jets and back	23
Best practices for time-resolved serial synchrotron crystallography	23
Crystal structures of human ENPP1 in apo and bound forms	23
Industrial cryo-EM facility setup and management	21
CCP4 Cloud for structure determination and project management in macromolecular crystallography	21
Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300	20

Optimized cryo-EM data-acquisition workflow by sample-thickness determination	20
New system for archiving integrative structures	19
Pre-clustering data sets using cluster4x improves the signal-to-noise ratio of high-throughput crystallography drug-screening analysis	18
Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion	17
Predicting protein model correctness in Coot using machine learning	17
Improving sampling of crystallographic disorder in ensemble refinement	17
On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy	16
Structural dynamics: review of time-resolved cryo-EM	16
The low-cost Shifter microscope stage transforms the speed and robustness of protein crystal harvesting	16
Accelerating crystal structure determination with iterative AlphaFold prediction	16
Making a difference in multi-data-set crystallography: simple and deterministic data-scaling/selection methods	16
Adaptive Cartesian and torsional restraints for interactive model rebuilding	16
On-grid and in-flow mixing for time-resolved cryo-EM	15
Determination of intracellular protein–ligand binding affinity by competition binding in-cell NMR	14
The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP	13
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models	13
ModelCraft: an advanced automated model-building pipeline using Buccaneer	13
Validation, analysis and annotation of cryo-EM structures	13
Homogeneous batch micro-crystallization of proteins from ammonium sulfate	13
Substrate binding in the bile acid transporter ASBTYffromYersinia frederiksenii	13
IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition	13
Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II–transducer complex	12
Crown-ether-mediated crystal structures of the glycosyltransferasePaGT3 fromPhytolacca americana	12
MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more	12
Structure of CYRI-B (FAM49B), a key regulator of cellular actin assembly	12
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking	12
Influence of the presence of the heme cofactor on the JK-loop structure in indoleamine 2,3-dioxygenase 1	12
Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org	12
A new inactive conformation of SARS-CoV-2 main protease	12
Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER	12
UnityMol prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments	12
Targeting the innate immune receptor TLR8 using small-molecule agents	12
Insight into the potential factors influencing the catalytic direction in cellobiose 2-epimerase by crystallization and mutagenesis	11
B-factor accuracy in protein crystal structures	11
The structure of natively iodinated bovine thyroglobulin	11
Fast fragment- and compound-screening pipeline at the Swiss Light Source	11
Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography	10
The missing link: covalent linkages in structural models	10
Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals	10
Bond-valence analyses of the crystal structures of FeMo/V cofactors in FeMo/V proteins	10
Crystal structure of human brain-type fatty acid-binding protein FABP7 complexed with palmitic acid	10
A GH13 α-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides	10
Phasertng: directed acyclic graphs for crystallographic phasing	10
High-resolution structures of the bound effectors avadomide (CC-122) and iberdomide (CC-220) highlight advantages and limitations of the MsCI4 soaking system	10
Shift-field refinement of macromolecular atomic models	10
Structures of full-length VanR from Streptomyces coelicolor in both the inactive and activated states	10
Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking	10
Low-resolution structures of modular nanotransporters shed light on their functional activity	10
Principal component analysis is limited to low-resolution analysis in cryoEM	10
Modelling covalent linkages in CCP4	10

Identification of Mg2+ ions next to nucleotides in cryo-EM maps using electrostatic potential maps	9
Local and global analysis of macromolecular atomic displacement parameters	9
A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip	9
Integrated sample-handling and mounting system for fixed-target serial synchrotron crystallography	9
Validation analysis of EMDB entries	9
Crystal and solution structures of fragments of the human leucocyte common antigen-related protein	9
Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography	9
The RING domain of TRIM69 promotes higher-order assembly	9
Macromolecular crystallography using microcrystal electron diffraction	9
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER	9
Ion permeation in potassium ion channels	9
The structure of Prp2 bound to RNA and ADP-BeF3−reveals structural features important for RNA unwinding by DEAH-box ATPases	9
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	9
FragMAXapp: crystallographic fragment-screening data-analysis and project-management system	9
Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips	9
Novel structure of the N-terminal helical domain of BibA, a group B streptococcus immunogenic bacterial adhesin	8
Inhibition of Schistosoma mansoni carbonic anhydrase by the antiparasitic drug clorsulon: X-ray crystallographic and in vitro studies	8
Molecular-dynamics simulation methods for macromolecular crystallography	8
Structural biology of coronavirus ion channels	8
Solution structure and assembly of β-amylase 2 fromArabidopsis thaliana	8
Structure of a GH51 α-L-arabinofuranosidase from Meripilus giganteus: conserved substrate recognition from bacteria to fungi	8
The crystal structure of the TonB-dependent transporter YncD reveals a positively charged substrate-binding site	8
Microsecond melting and revitrification of cryo samples: protein structure and beam-induced motion	8
Structural and biochemical characterization of the novel serpin Iripin-5 from Ixodes ricinus	8
Vagabond: bond-based parametrization reduces overfitting for refinement of proteins	8
Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization	8
Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy	8
Native SAD phasing at room temperature	8
Ice in biomolecular cryocrystallography	8
Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals	8
Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching	8
Structural and thermodynamic analyses of interactions between death-associated protein kinase 1 and anthraquinones	8
The three-dimensional structure of Drosophila melanogaster (6–4) photolyase at room temperature	7
Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method	7
HomogeneouslyN-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis	7
How do I get the most out of my protein sequence using bioinformatics tools?	7
Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain	7
Atomic model validation using the CCP-EM software suite	7
Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae	7
Arginine off-kilter: guanidinium is not as planar as restraints denote	7
Versatile microporous polymer-based supports for serial macromolecular crystallography	7
Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0	7
Using RELION software within the Scipion framework	7
Improving data quality and expanding BioSAXS experiments to low-molecular-weight and low-concentration protein samples	7
Real-space quantum-based refinement for cryo-EM: Q|R#3	7
Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization	6
Real space in cryo-EM: the future is local	6
Structural and biochemical characterization of novel carbonic anhydrases fromPhaeodactylum tricornutum	6
Mycobacterium tuberculosis ferritin: a suitable workhorse protein for cryo-EM development	6
Structure of apo flavin-dependent halogenase Xcc4156 hints at a reason for cofactor-soaking difficulties	6
Structure–functional relationship of cellular retinoic acid-binding proteins I and II interacting with natural and synthetic ligands	6
Structural insights into the interaction of papain-like protease 2 from the alphacoronavirus porcine epidemic diarrhea virus and ubiquitin	6
The parallel-stranded d(CGA) duplex is a highly predictable structural motif with two conformationally distinct strands	6
Recent structural insights into the mechanism of lysozyme hydrolysis	6
High-throughput in situ experimental phasing	6
Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel	6
Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre	6
Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase	6
Updated restraint dictionaries for carbohydrates in the pyranose form	6
Structural visualization of transient interactions between the cis-acting acyltransferase and acyl carrier protein of the salinomycin modular polyketide synthase	6
Sequence-assignment validation in cryo-EM models with checkMySequence	6
Likelihood-based docking of models into cryo-EM maps	6
Using deep-learning predictions of inter-residue distances for model validation	6
High-resolution crystal structure of Trypanosoma brucei pteridine reductase 1 in complex with an innovative tricyclic-based inhibitor	6
Crystal structure of fungal tannase from Aspergillus niger	6
Structure and metal-binding properties of PA4063, a novel player in periplasmic zinc trafficking byPseudomonas aeruginosa	6
The crystal structure of CbpD clarifies substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases	6
CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures	6
A solution-free crystal-mounting platform for native SAD	5
New restraints and validation approaches for nucleic acid structures in PDB-REDO	5
Structural insights into the substrate-binding cleft of AlyF reveal the first long-chain alginate-binding mode	5
Structure of a C1/C4-oxidizing AA9 lytic polysaccharide monooxygenase from the thermophilic fungus Malbranchea cinnamomea	5
Structural basis of the dominant inheritance of hypermethioninemia associated with the Arg264His mutation in the MAT1A gene	5
A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs	5
Development and assessment of CootVR, a virtual reality computer program for model building	5
Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum	5
Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6	5
LAHMA: structure analysis through local annotation of homology-matched amino acids	5
Theoretical 3D electron diffraction electrostatic potential maps of proteins modeled with a multipolar pseudoatom data bank	5
The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2	5

Structural analysis of the PATZ1 BTB domain homodimer	5
Insulin polymorphism induced by two polyphenols: new crystal forms and advances in macromolecular powder diffraction	5
Visualizing an unseen enemy; mobilizing structural biology to counter COVID-19	5
Serial femtosecond X-ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase	5
Structural basis for substrate recognition in the Phytolacca americana glycosyltransferase PaGT3	5
Room-temperature serial synchrotron crystallography of Drosophila cryptochrome	5
Recognition of an α-helical hairpin in P22 large terminase by a synthetic antibody fragment	5
High-resolution structure determination using high-throughput electron cryo-tomography	5
Entropic pressure controls the oligomerization of the Vibrio cholerae ParD2 antitoxin	5
Structural basis of carbohydrate binding in domain C of a type I pullulanase fromPaenibacillus barengoltzii	5
Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score	5
C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening	5
Crystal structure of bacteriophage T4 Spackle as determined by native SAD phasing	4
The BAM7 gene in Zea mays encodes a protein with similar structural and catalytic properties to Arabidopsis BAM2	4
Crystallographic binding studies of rat peroxisomal multifunctional enzyme type 1 with 3-ketodecanoyl-CoA: capturing active and inactive states of its hydratase and dehydrogenase catalytic sites	4
Structural and binding studies of a new chitin-active AA10 lytic polysaccharide monooxygenase from the marine bacterium Vibrio campbellii	4
Structural analysis of the sulfatase AmAS from Akkermansia muciniphila	4
Structure of P46, an immunodominant surface protein fromMycoplasma hyopneumoniae: interaction with a monoclonal antibody	4
AutoPX: a new software package to process X-ray diffraction data from biomacromolecular crystals	4
Detection of translational noncrystallographic symmetry in Patterson functions	4
A rush to explore protein–ligand electrostatic interaction energy with Charger	4
Structural analysis of LpqY, a substrate-binding protein from the SugABC transporter of Mycobacterium tuberculosis, provides insights into its trehalose specificity	4
Crystal structures of adenylylated and unadenylylated PIIprotein GlnK fromCorynebacterium glutamicum	4
In situ ligand restraints from quantum-mechanical methods	4
Data collection from crystals grown in microfluidic droplets	4
Announcing the launch of Protein Data Bank China as an Associate Member of the Worldwide Protein Data Bank Partnership	4
Exiting the tunnel of uncertainty: crystal soak to validated hit	4
GEMMI and Servalcat restrain REFMAC5	4
Ab initio determination of the shape of membrane proteins in a nanodisc	4
Correlative cryo-imaging of the cellular universe with soft X-rays and laser light used to track F-actin structures in mammalian cells	4
Structure and functional properties of the cold-adapted catalase from Acinetobacter sp. Ver3 native to the Atacama plateau in northern Argentina	4
Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography	4
Crystal structure of the putative cell-wall lipoglycan biosynthesis protein LmcA fromMycobacterium smegmatis	4
A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography	4
Ten things I `hate' about refinement	4
Determining the oxidation state of elements by X-ray crystallography	4
Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned	4
A baculoviral system for the production of human β-glucocerebrosidase enables atomic resolution analysis	4
Automated orientation of water molecules in neutron crystallographic structures of proteins	3
Databases for intrinsically disordered proteins	3
Crystal structures of UDP-N-acetylmuramic acid L-alanine ligase (MurC) from Mycobacterium bovis with and without UDP-N-acetylglucosamine	3
Control of strain in subgrains of protein crystals by the introduction of grown-in dislocations	3
Introduction to molecular replacement: a time perspective	3
Structure and mechanism of the γ-glutamyl-γ-aminobutyrate hydrolase SpuA from Pseudomonas aeruginosa	3
The suppressor of copper sensitivity protein C from Caulobacter crescentus is a trimeric disulfide isomerase that binds copper(I) with subpicomolar affinity	3
An engineered disulfide bridge traps and validates an outward-facing conformation in a bile acid transporter	3
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	3
Radiation-induced defects in protein crystals observed by X-ray topography	3
Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family	3
Errors in structural biology are not the exception	3
Molecular insight into 2-phosphoglycolate activation of the phosphatase activity of bisphosphoglycerate mutase	3
Crystallization, structural characterization and kinetic analysis of a GH26 β-mannanase from Klebsiella oxytoca KUB-CW2-3	3
Structural studies of hemoglobin from two flightless birds, ostrich and turkey: insights into their differing oxygen-binding properties	3
Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure	3
Estimating local protein model quality: prospects for molecular replacement	3
Glycoside hydrolase family 5: structural snapshots highlighting the involvement of two conserved residues in catalysis	3
Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM	3
Integrated, rational molecular replacement	3
Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures	3
Flipping the substrate preference of Hazara virus ovarian tumour domain protease through structure-based mutagenesis	3
Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap	3
Structural and spectrophotometric investigation of two unnatural amino-acid altered chromophores in the superfolder green fluorescent protein	3
A scalable strategy to solve structures of PDZ domains and their complexes	3
Synergic action of an inserted carbohydrate-binding module in a glycoside hydrolase family 5 endoglucanase	3
Catalytically active holoHomo sapiensadenosine deaminase I adopts a closed conformation	3
Development of CryoVR, a virtual reality training system for hands-on cryoEM operations	3
AlphaFold and the future of structural biology	3
Crystal structure of a polyglycine hydrolase determined using a RoseTTAFold model	3
Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM	3
Global fitting of multiple data frames from SEC–SAXS to investigate the structure of next-generation nanodiscs	3
The impact of folding modes and deuteration on the atomic resolution structure of hen egg-white lysozyme	3
Crystal structures of the molecular class A β-lactamase TEM-171 and its complexes with tazobactam	3
Towards the automatic crystal structure solution of nucleic acids: automated model building using the new CAB program	3
Structural basis of regioselective tryptophan dibromination by the single-component flavin-dependent halogenase AetF	3
Structure–function study of AKR4C14, an aldo-keto reductase from Thai jasmine rice (Oryza sativaL. ssp.indicacv. KDML105)	3
Crystal structure of a covalently linked Aurora-A–MYCN complex	3
Analysis and validation of overall N-glycan conformation in Privateer	3
Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase	3
Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase	3
Exploring ligand dynamics in protein crystal structures with ensemble refinement	3
Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks	3
Direct calculation of cryo-EM and crystallographic model maps for real-space refinement	3
Detecting ice artefacts in processed macromolecular diffraction data with machine learning	3
The TR-icOS setup at the ESRF: time-resolved microsecond UV–Vis absorption spectroscopy on protein crystals	2
SCOMAP-XD: atomistic deuterium contrast matching for small-angle neutron scattering in biology	2
Lysozyme crystals dyed with bromophenol blue: where has the dye gone?	2
Protonation states of hen egg-white lysozyme observed using D/H contrast neutron crystallography	2
Evaluating crystallographic likelihood functions using numerical quadratures	2
Exploring the complex map of insulin polymorphism: a novel crystalline form in the presence ofm-cresol	2
Structure of Thermococcus litoralis Δ1-pyrroline-2-carboxylate reductase in complex with NADH and L-proline	2
Leishmania major biotin protein ligase forms a unique cross-handshake dimer	2
Likelihood-based signal and noise analysis for docking of models into cryo-EM maps	2
Crystal structure of anNω-hydroxy-L-arginine hydrolase found in theD-cycloserine biosynthetic pathway	2
Near-atomic resolution reconstructions from in situ revitrified cryo samples	2
Native glycosylation and binding of the antidepressant paroxetine in a low-resolution crystal structure of human myeloperoxidase	2