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Towards automated crystallographic structure refinement with phenix.refine

Journal Article · · Acta Crystallographica. Section D: Biological Crystallography
 [1];  [2];  [2];  [2];  [2];  [3];  [3];  [4];  [2];  [5]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); DOE/OSTI
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  4. Centre National de la Recherche Scientifique (CNRS), Illkirch (France). INSERM. UdS. IGBMC; Univ. Henri Poincare, Nancy (France). Faculte des Sciences et des TechnologiesDept. de Physique
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
+ Show Author Affiliations

phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Institutes of Health (NIH)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1625674
Alternate ID(s):
OSTI ID: 1810133
OSTI ID: 22347876
Journal Information:
Acta Crystallographica. Section D: Biological Crystallography, Journal Name: Acta Crystallographica. Section D: Biological Crystallography Journal Issue: 4 Vol. 68; ISSN 0907-4449
Publisher:
International Union of CrystallographyCopyright Statement
Country of Publication:
United States
Language:
English

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XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining journal October 2018
Structures of the ISWI–nucleosome complex reveal a conserved mechanism of chromatin remodeling journal March 2019
Receptor subtype discrimination using extensive shape complementary designed interfaces journal May 2019
Structural basis of temperature sensation by the TRP channel TRPV3 journal October 2019
Structure of the human TRiC/CCT Subunit 5 associated with hereditary sensory neuropathy journal June 2017
Towards high throughput GPCR crystallography: In Meso soaking of Adenosine A2A Receptor crystals journal January 2018
Crystal structure of a Ca2+-dependent regulator of flagellar motility reveals the open-closed structural transition journal January 2018
Structural cycle of the Thermus thermophilus PilF ATPase: the powering of type IVa pilus assembly journal September 2018
Biochemical and structural characterization of tomato polyphenol oxidases provide novel insights into their substrate specificity journal March 2019
An engineered GH1 β-glucosidase displays enhanced glucose tolerance and increased sugar release from lignocellulosic materials journal March 2019
Specific modification at the C-terminal lysine residue of the green fluorescent protein variant, GFPuv, expressed in Escherichia coli journal March 2019
Structural determinants of inhibition of Porphyromonas gingivalis gingipain K by KYT-36, a potent, selective, and bioavailable peptidase inhibitor journal March 2019
Characterization of metal binding of bifunctional kinase/phosphatase AceK and implication in activity modulation journal June 2019
Non-Contact Universal Sample Presentation for Room Temperature Macromolecular Crystallography Using Acoustic Levitation journal August 2019
Crystal structure of ErmE - 23S rRNA methyltransferase in macrolide resistance journal October 2019
Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models journal December 2019
Capture and characterization of a reactive haem–carbenoid complex in an artificial metalloenzyme journal July 2018
Unexpected enzyme-catalysed [4+2] cycloaddition and rearrangement in polyether antibiotic biosynthesis journal October 2019
Flagella-mediated secretion of a novel Vibrio cholerae cytotoxin affecting both vertebrate and invertebrate hosts journal June 2018
Structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase reveals mechanism of substrate binding and metal catalysis journal May 2019
Insights into the κ/ι-carrageenan metabolism pathway of some marine Pseudoalteromonas species journal December 2019
Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation journal February 2020
Structural analysis of fungus-derived FAD glucose dehydrogenase journal August 2015
Mechanistic insights into the recognition of 5-methylcytosine oxidation derivatives by the SUVH5 SRA domain journal February 2016
Structural characterisation of human galectin-4 N-terminal carbohydrate recognition domain in complex with glycerol, lactose, 3′-sulfo-lactose and 2′-fucosyllactose journal February 2016
Ringhalexin from Hemachatus haemachatus: A novel inhibitor of extrinsic tenase complex journal May 2016
Structural and biochemical characterization of the cell fate determining nucleotidyltransferase fold protein MAB21L1 journal June 2016
Chalcogenide substitution in the [2Fe] cluster of [FeFe]-hydrogenases conserves high enzymatic activity journal January 2017
A functional interplay between intein and extein sequences in protein splicing compensates for the essential block B histidine journal January 2019
Structural insights reveal a recognition feature for tailoring hydrocarbon stapled-peptides against the eukaryotic translation initiation factor 4E protein journal January 2019
Routes of iron entry into, and exit from, the catalytic ferroxidase sites of the prokaryotic ferritin Syn Ftn journal January 2020
Thymine DNA glycosylase recognizes the geometry alteration of minor grooves induced by 5-formylcytosine and 5-carboxylcytosine journal January 2019
Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a Paenibacillus sp. IK-5 chitosanase/glucanase journal April 2016
Specificity and mechanism of carbohydrate demethylation by cytochrome P450 monooxygenases journal December 2018
Structure and nucleotide-induced conformational dynamics of the Chlorobium tepidum Roco protein journal January 2019
Crystal structures of plant inorganic pyrophosphatase, an enzyme with a moonlighting autoproteolytic activity journal August 2019
Crystal structure of the FRP and identification of the active site for modulation of OCP-mediated photoprotection in cyanobacteria journal May 2013
Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling journal July 2013
Protein crystal structure obtained at 2.9 A resolution from injecting bacterial cells into an X-ray free-electron laser beam journal August 2014
Structure of deformed wing virus, a major honey bee pathogen journal March 2017
Comprehensive understanding of acetohydroxyacid synthase inhibition by different herbicide families journal January 2017
Potent neutralization of hepatitis A virus reveals a receptor mimic mechanism and the receptor recognition site journal January 2017
Structure of eukaryotic CMG helicase at a replication fork and implications to replisome architecture and origin initiation journal January 2017
Accurate model annotation of a near-atomic resolution cryo-EM map journal March 2017
Affimer proteins inhibit immune complex binding to FcγRIIIa with high specificity through competitive and allosteric modes of action journal December 2017
Capturing LTA 4 hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB 4 synthesis journal August 2017
Aminoglycoside interactions and impacts on the eukaryotic ribosome journal December 2017
Crystal structures of a [NiFe] hydrogenase large subunit HyhL in an immature state in complex with a Ni chaperone HypA journal June 2018
Broadly conserved Na + -binding site in the N-lobe of prokaryotic multidrug MATE transporters journal June 2018
MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat journal December 2018
Reaction of O 2 with a diiron protein generates a mixed-valent Fe 2+ /Fe 3+ center and peroxide journal January 2019
Structural determinants driving homoserine lactone ligand selection in the Pseudomonas aeruginosa LasR quorum-sensing receptor journal December 2018
Unsupervised determination of protein crystal structures journal May 2019
Solving the structure of Lgl2, a difficult blind test of unsupervised structure determination journal May 2019
Crystal structure of cis -aconitate decarboxylase reveals the impact of naturally occurring human mutations on itaconate synthesis journal September 2019
Overcoming insecticide resistance through computational inhibitor design journal October 2019
Insights into the mechanism and regulation of the CbbQO-type Rubisco activase, a MoxR AAA+ ATPase journal December 2019
Structural basis of exo-β-mannanase activity in the GH2 family journal August 2018
Cryo-EM structure of the cytoplasmic domain of murine transient receptor potential cation channel subfamily C member 6 (TRPC6) journal June 2018
Disulfide engineering of human Kunitz-type serine protease inhibitors enhances proteolytic stability and target affinity toward mesotrypsin journal January 2019
Substrate N2 atom recognition mechanism in pierisin family DNA-targeting, guanine-specific ADP-ribosyltransferase ScARP journal September 2018
Large Scale Structural Rearrangement of a Serine Hydrolase from Francisella tularensis Facilitates Catalysis* journal April 2013
Identification, Structure, and Function of a Novel Type VI Secretion Peptidoglycan Glycoside Hydrolase Effector-Immunity Pair journal July 2013
Cocrystal Structures of Glycyl-tRNA Synthetase in Complex with tRNA Suggest Multiple Conformational States in Glycylation journal June 2014
Borrelia burgdorferi Protein BBK32 Binds to Soluble Fibronectin via the N-terminal 70-kDa Region, Causing Fibronectin to Undergo Conformational Extension journal June 2014
Two Putative Polysaccharide Deacetylases Are Required for Osmotic Stability and Cell Shape Maintenance in Bacillus anthracis journal May 2015
Two-step Ligand Binding in a (βα)8 Barrel Enzyme journal October 2015
Structural Basis for Clonal Diversity of the Public T Cell Response to a Dominant Human Cytomegalovirus Epitope journal October 2015
Molecular Basis of Enhanced Activity in Factor VIIa-Trypsin Variants Conveys Insights into Tissue Factor-mediated Allosteric Regulation of Factor VIIa Activity journal February 2016
The Structure of the Transcriptional Repressor KstR in Complex with CoA Thioester Cholesterol Metabolites Sheds Light on the Regulation of Cholesterol Catabolism in Mycobacterium tuberculosis journal April 2016
Bacillus anthracis Prolyl 4-Hydroxylase Modifies Collagen-like Substrates in Asymmetric Patterns journal June 2016
A unique structural domain in Methanococcoides burtonii ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) acts as a small subunit mimic journal April 2017
Structure–function analyses reveal key features in Staphylococcus aureus IsdB-associated unfolding of the heme-binding pocket of human hemoglobin journal November 2017
Structure–function analyses of a stereotypic rheumatoid factor unravel the structural basis for germline-encoded antibody autoreactivity journal March 2018
Structural analyses of Arabidopsis thaliana legumain γ reveal differential recognition and processing of proteolysis and ligation substrates journal June 2018
Diverse NADase effector families mediate interbacterial antagonism via the type VI secretion system journal December 2017
The invasin D protein from Yersinia pseudotuberculosis selectively binds the Fab region of host antibodies and affects colonization of the intestine journal March 2018
AMP-activated protein kinase selectively inhibited by the type II inhibitor SBI-0206965 journal June 2018
Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding journal September 2018
Structural mechanism of AadA, a dual-specificity aminoglycoside adenylyltransferase from Salmonella enterica journal July 2018
Crystal structure of the TreS:Pep2 complex, initiating α-glucan synthesis in the GlgE pathway of mycobacteria journal May 2019
Crystal structure of the WFIKKN2 follistatin domain reveals insight into how it inhibits growth differentiation factor 8 (GDF8) and GDF11 journal April 2019
Heat shock protein 104 (HSP104) chaperones soluble Tau via a mechanism distinct from its disaggregase activity journal March 2019
A mutually induced conformational fit underlies Ca2+-directed interactions between calmodulin and the proximal C terminus of KCNQ4 K+ channels journal April 2019
Structural analysis of a Vibrio phospholipase reveals an unusual Ser–His–chloride catalytic triad journal July 2019
Beating tissue factor at its own game: Design and properties of a soluble tissue factor–independent coagulation factor VIIa journal January 2020
REV7 has a dynamic adaptor region to accommodate small GTPase RAN/ Shigella IpaB ligands, and its activity is regulated by the RanGTP/GDP switch journal September 2019
Characterizing pathological imperfections in macromolecular crystals: lattice disorders and modulations journal December 2019
Bisubstrate analogues as structural tools to investigate m 6 A methyltransferase active sites journal March 2019
Structural basis of Type IV CRISPR RNA biogenesis by a Cas6 endoribonuclease journal June 2019
Structures of the yeast dynamin-like GTPase Sey1p provide insight into homotypic ER fusion journal September 2015
Structures of human mitofusin 1 provide insight into mitochondrial tethering journal December 2016
Structures of the fungal dynamin-related protein Vps1 reveal a unique, open helical architecture journal August 2018
Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis journal November 2017
The phage T4 MotA transcription factor contains a novel DNA binding motif that specifically recognizes modified DNA journal April 2018
TraN: A novel repressor of an Enterococcus conjugative type IV secretion system journal July 2018
Structural insights into DNA degradation by human mitochondrial nuclease MGME1 journal September 2018
Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome journal February 2019
Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1 journal December 2019
Crystal structure of human cytoplasmic tRNAHis-specific 5′-monomethylphosphate capping enzyme journal January 2020
NMR solution and X-ray crystal structures of a DNA molecule containing both right- and left-handed parallel-stranded G-quadruplexes journal June 2019
Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine journal May 2019
Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening journal June 2019
Structural and functional insight into the Mycobacterium tuberculosis protein PrpR reveals a novel type of transcription factor journal August 2019
Structure and function of the Toscana virus cap-snatching endonuclease journal October 2019
Adhiron: a stable and versatile peptide display scaffold for molecular recognition applications journal March 2014
A novel mutation alters the stability of PapA2 resulting in the complete abrogation of sulfolipids in clinical mycobacterial strains journal April 2019
Structural variability of EspG chaperones from mycobacterial ESX-1, ESX-3 and ESX-5 type VII secretion systems posted_content October 2018
Dynamics of human protein kinases linked to drug selectivity posted_content March 2018
Common antigenic motif recognized by human VH5-51/VL4-1 tau antibodies with distinct functionalities posted_content January 2018
MMOD-induced structural changes of hydroxylase in soluble methane monooxygenase posted_content May 2018
Eradication of ENO1 -deleted Glioblastoma through Collateral Lethality posted_content January 2018
Structural basis for σ 1 receptor ligand recognition journal June 2018
Collection of continuous rotation MicroED Data from Ion Beam Milled Crystals of Any Size journal September 2018
Atomic view into Plasmodium actin polymerization, ATP hydrolysis, and phosphate release posted_content January 2018
A structure-based model for the electrostatic interaction of the N-terminus of protein tau with the fibril core of Alzheimer’s Disease filaments posted_content January 2018
A novel mutation alters the stability of PapA2 resulting in the complete abrogation of sulfolipids in clinical mycobacterial strains posted_content January 2018
Crystal structure of the LRR ectodomain of the plant immune receptor kinase SOBIR1 posted_content January 2019
Crystal structures of the outer membrane transporter FoxA provide novel insights into TonB-mediated siderophore uptake and signalling posted_content January 2019
Structural and functional characterisation of SiiA, an auxiliary protein from the SPI4-encoded type 1 secretion system from Salmonella enterica posted_content January 2019
In-vivo crystals reveal protein interactions posted_content January 2019
Structural basis of transcription inhibition by the DNA mimic protein Ocr of bacteriophage T7 journal October 2019
Conservation of the structure and function of bacterial tryptophan synthases journal May 2019
Bulk-solvent and overall scaling revisited: faster calculations, improved results journal March 2013
Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data journal June 2013
New model-fitting and model-completion programs for automated iterative nucleic acid refinement journal May 2013
Structure of γ-conglutin: insight into the quaternary structure of 7S basic globulins from legumes journal January 2015
Snapshots of ligand entry, malleable binding and induced helical movement in P-glycoprotein journal February 2015
Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3,4 domains of integrin α6β4 journal March 2015
Structure–function relationships in Gan42B, an intracellular GH42 β-galactosidase from Geobacillus stearothermophilus journal November 2015
BraggNet: integrating Bragg peaks using neural networks text January 2019
IPCAS : a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination journal February 2020
Conformational variation of proteins at room temperature is not dominated by radiation damage journal January 2017
Serial femtosecond crystallography of soluble proteins in lipidic cubic phase journal August 2015
Synchrotron microcrystal native-SAD phasing at a low energy journal May 2019
Room-temperature photo-induced martensitic transformation in a protein crystal journal May 2019
Formation of a highly dense tetra-rhenium cluster in a protein crystal and its implications in medical imaging journal June 2019
The structure of hookworm platelet inhibitor (HPI), a CAP superfamily member from Ancylostoma caninum journal May 2015
Structure of the HIV-1 reverse transcriptase Q151M mutant: insights into the inhibitor resistance of HIV-1 reverse transcriptase and the structure of the nucleotide-binding pocket ofHepatitis B viruspolymerase journal October 2015
New crystal form of human ubiquitin in the presence of magnesium journal January 2016
The first crystal structure of manganese superoxide dismutase from the genus Staphylococcus journal February 2018
Improved protein-crystal identification by using 2,2,2-trichloroethanol as a fluorescence enhancer journal April 2018
Crystallization and X-ray analysis of all of the players in the autoregulation of the ataRT toxin–antitoxin system journal June 2018
Neutron and X-ray crystal structures of Lactobacillus brevis alcohol dehydrogenase reveal new insights into hydrogen-bonding pathways journal November 2018
Crystal structure of the type VI immunity protein Tdi1 (Atu4351) from Agrobacterium tumefaciens journal February 2019
The putative polysaccharide deacetylase Ba0331: cloning, expression, crystallization and structure determination journal April 2019
Crystal structure of the glycoside hydrolase PssZ from Listeria monocytogenes journal June 2019
The crystal structure of haemoglobin from Atlantic cod journal July 2019
The Rel stringent factor from Thermus thermophilus : crystallization and X-ray analysis journal August 2019
Major conformational changes in the structure of lysozyme obtained from a crystal with a very low solvent content journal November 2019
The anatomy of a comprehensive constrained, restrained refinement program for the modern computing environment – Olex2 dissected journal January 2015
MicroED data collection and processing journal July 2015
Microcrystal delivery by pulsed liquid droplet for serial femtosecond crystallography journal March 2016
Discovery of a novel allosteric inhibitor-binding site in ERK5: comparison with the canonical kinase hinge ATP-binding site journal April 2016
An editor for the generation and customization of geometry restraints journal February 2017
Macromolecular refinement by model morphing using non-atomic parameterizations journal February 2018
Structure and function of the type III pullulan hydrolase from Thermococcus kodakarensis journal April 2018
MR-REX : molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models journal June 2018
Real-space refinement in PHENIX for cryo-EM and crystallography journal May 2018
Structures of two fimbrial adhesins, AtfE and UcaD, from the uropathogen Proteus mirabilis journal October 2018
Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space journal October 2018
Iron–sulfur clusters have no right angles journal January 2019
Conformational changes in the third PDZ domain of the neuronal postsynaptic density protein 95 journal March 2019
Crystal structure of the leucine-rich repeat ectodomain of the plant immune receptor kinase SOBIR1 journal April 2019
Structure of the N-terminal domain of Euprosthenops australis dragline silk suggests that conversion of spidroin dope to spider silk involves a conserved asymmetric dimer intermediate text January 2019
Combining random microseed matrix screening and the magic triangle for the efficient structure solution of a potential lysin from bacteriophage P68 text January 2019
Crystal structures of the closed form of Mycobacterium tuberculosis dihydrofolate reductase in complex with dihydrofolate and antifolates journal July 2019
X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein journal August 2019
The flavin mononucleotide cofactor in α-hydroxyacid oxidases exerts its electrophilic/nucleophilic duality in control of the substrate-oxidation level journal September 2019
Identifying dynamic, partially occupied residues using anomalous scattering journal November 2019
Structure and mechanism of piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus journal November 2019
Comparison of automated crystallographic model-building pipelines journal November 2019
Catalytic mechanism and evolutionary characteristics of thioredoxin from Halobacterium salinarum NRC-1 journal January 2020
Structural and catalytic effects of proline substitution and surface loop deletion in the extended active site of human carbonic anhydrase II journal March 2015
High-resolution studies of hydride transfer in the ferredoxin:NADP + reductase superfamily journal August 2017
Structural basis for PDZ domain interactions in the post-synaptic density scaffolding protein Shank3 journal June 2018
Crystal structure and catalytic activity of the PPM1K N94K mutant journal January 2019
Interface interactions between βγ-crystallin domain and Ig-like domain render Ca 2+ -binding site inoperative in abundant perithecial protein of Neurospora crassa: Regulation of Ca 2+ binding by interdomain interface journal October 2018
Molecular insights into the master regulator CysB‐mediated bacterial virulence in Pseudomonas aeruginosa journal March 2019
Crystal structures of rhamnosyltransferase UGT 89C1 from Arabidopsis thaliana reveal the molecular basis of sugar donor specificity for UDP ‐β‐ l ‐rhamnose and rhamnosylation mechanism journal April 2019
A low-barrier hydrogen bond mediates antibiotic resistance in a noncanonical catalytic triad journal April 2018
Mechanism of calmodulin inactivation of the calcium-selective TRP channel TRPV6 journal August 2018
MMOD-induced structural changes of hydroxylase in soluble methane monooxygenase journal October 2019
Solving a new R2lox protein structure by microcrystal electron diffraction journal August 2019
A Structurally Distinct Human Mycoplasma Protein that Generically Blocks Antigen-Antibody Union journal February 2014
Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli journal August 2014
Structural basis for organohalide respiration journal October 2014
Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor journal March 2015
A stable trimeric influenza hemagglutinin stem as a broadly protective immunogen journal August 2015
Design of structurally distinct proteins using strategies inspired by evolution journal May 2016
The 3.8 A resolution cryo-EM structure of Zika virus journal March 2016
Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell journal June 2017
Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks journal February 2018
Structures of the CRISPR genome integration complex journal July 2017
Crystal structure of the human lysosomal mTORC1 scaffold complex and its impact on signaling journal September 2017
Fibril structure of amyloid-β(1–42) by cryo–electron microscopy journal September 2017
Cryo-EM structure of a herpesvirus capsid at 3.1 Å journal April 2018
Mechanism of β 2 AR regulation by an intracellular positive allosteric modulator journal June 2019
Architecture of African swine fever virus and implications for viral assembly journal October 2019
Functional Profiling and Crystal Structures of Isothiocyanate Hydrolases Found in Gut-Associated and Plant-Pathogenic Bacteria journal May 2018
Glucan Binding Protein C of Streptococcus mutans Mediates both Sucrose-Independent and Sucrose-Dependent Adherence journal April 2018
Selective Utilization of Benzimidazolyl-Norcobamides as Cofactors by the Tetrachloroethene Reductive Dehalogenase of Sulfurospirillum multivorans journal January 2018
Structural Differences between the Woodchuck Hepatitis Virus Core Protein in the Dimer and Capsid States Are Consistent with Entropic and Conformational Regulation of Assembly journal July 2019
Structural Insight into African Swine Fever Virus A179L-Mediated Inhibition of Apoptosis journal January 2017
The Megavirus Chilensis Cu,Zn-Superoxide Dismutase: the First Viral Structure of a Typical Cellular Copper Chaperone-Independent Hyperstable Dimeric Enzyme journal October 2014
Structural and In Vivo Studies on Trehalose-6-Phosphate Synthase from Pathogenic Fungi Provide Insights into Its Catalytic Mechanism, Biological Necessity, and Potential for Novel Antifungal Drug Design journal July 2017
Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the β barrel in fatty acid binding proteins journal June 2018
The mechanism by which a distinguishing arabinofuranosidase can cope with internal di-substitutions in arabinoxylans journal August 2018
Biochemical and structural features of diverse bacterial glucuronoyl esterases facilitating recalcitrant biomass conversion journal August 2018
Nucleobase carbonyl groups are poor Mg 2+ inner-sphere binders but excellent monovalent ion binders—a critical PDB survey journal November 2018
Structural Basis of Rap Phosphatase Inhibition by Phr Peptides journal March 2013
Structural basis for neutralization of hepatitis A virus informs a rational design of highly potent inhibitors journal April 2019
The Pilin Protein FimP from Actinomyces oris: Crystal Structure and Sequence Analyses journal October 2012
High-Resolution Structure of the N-Terminal Endonuclease Domain of the Lassa Virus L Polymerase in Complex with Magnesium Ions journal February 2014
Crystal Structure of the Stress-Inducible Human Heat Shock Protein 70 Substrate-Binding Domain in Complex with Peptide Substrate journal July 2014
Crystal structure and insights into the oligomeric state of UDP-glucose pyrophosphorylase from sugarcane journal March 2018
A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes journal May 2018
Molecular basis for functional diversity among microbial Nep1-like proteins journal September 2019
Structural evidence for the critical role of the prion protein hydrophobic region in forming an infectious prion journal December 2019
Structural and functional dissection of the interplay between lipid and Notch binding by human Notch ligands journal June 2017
High‐resolution archaellum structure reveals a conserved metal‐binding site journal March 2019
Serial protein crystallography in an electron microscope text January 2020
A high affinity RIM-binding protein/Aplip1 interaction prevents the formation of ectopic axonal active zones text January 2015
Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins text January 2019
An engineered GH1 β-glucosidase displays enhanced glucose tolerance and increased sugar release from lignocellulosic materials. text January 2019
Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase. text January 2015
Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA text January 2013
Crystal structures of disordered Z-type helices text January 2019
Serial femtosecond crystallography of soluble proteins in lipidic cubic phase text January 2015
Structure of AadA from Salmonella enterica : a monomeric aminoglycoside (3′′)(9) adenyltransferase text January 2015
Architecture and mechanism of the late endosomal Rab7-like Ypt7 guanine nucleotide exchange factor complex Mon1–Ccz1 text January 2017
Molecular mechanisms of Charcot-Marie-Tooth neuropathy linked to mutations in human myelin protein P2 text January 2017
Megahertz serial crystallography text January 2018
Convergent evolution in the mechanisms of ACBD3 recruitment to picornavirus replication sites text January 2019
Ultracompact 3D microfluidics for time-resolved structural biology text January 2020
Serial protein crystallography in an electron microscope text January 2020
Identification and Crystallographic Analysis of a New Carbohydrate Acetylesterase (SmAcE1) from Sinorhizobium meliloti journal January 2018
Conformational Flexibility of Proteins Involved in Ribosome Biogenesis: Investigations via Small Angle X-ray Scattering (SAXS) journal February 2018
Crystal Structure of Bovine Alpha-Chymotrypsin in Space Group P65 journal December 2018
A Novel Substrate-Binding Site in the X-ray Structure of an Oxidized E. coli Glyceraldehyde 3-Phosphate Dehydrogenase Elucidated by Single-Wavelength Anomalous Dispersion journal November 2019
Crystal Structure of Human EOLA1 Implies Its Possibility of RNA Binding journal September 2019
3-Substituted 1-Naphthamidomethyl-C-galactosyls Interact with Two Unique Sub-Sites for High-Affinity and High-Selectivity Inhibition of Galectin-3 journal December 2019
Molecular basis of AKAP79 regulation by calmodulin text January 2017
Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis text January 2019
Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC text January 2019
Acidic pH and divalent cation sensing by PhoQ are dispensable for systemic salmonellae virulence journal May 2015
Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli journal January 2016
A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria journal July 2017
Self-capping of nucleoprotein filaments protects the Newcastle disease virus genome journal July 2019
A high affinity RIM-binding protein/Aplip1 interaction prevents the formation of ectopic axonal active zones journal August 2015
Structure and in situ organisation of the Pyrococcus furiosus archaellum machinery journal June 2017
Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima journal April 2018
Structure of the human lipid-gated cation channel TRPC3 journal May 2018
Structure of mouse protocadherin 15 of the stereocilia tip link in complex with LHFPL5 journal August 2018
Molecular basis of synaptic specificity by immunoglobulin superfamily receptors in Drosophila journal January 2019
Architectural principles for Hfq/Crc-mediated regulation of gene expression journal February 2019
Binding and transport of D-aspartate by the glutamate transporter homolog GltTk journal April 2019

Figures / Tables (8)

Figure 1(p. 4)figure Figure 1
Figure 2(p. 7)figure Figure 2
Figure 3(p. 8)figure Figure 3
Table 1(p. 9)table Table 1
Figure 4(p. 10)figure Figure 4
Figure 5(p. 11)figure Figure 5
Figure 6(p. 12)figure Figure 6
Figure 7(p. 13)figure Figure 7

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
PHENIX
NCS
TLS
biochemistry & molecular biology
biophysics
crystallography
joint x-ray/neutron refinement
maximum likelihood
real-space refinement
simulated annealing
structure refinement
subatomic resolution
twinning