J. Appl. Cryst.の発刊に際して

Recent advances in the field of electron cryo-microscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of bio-macromolecules solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically for cryo-EM validation are required. We discuss new computational methods and tools implemented in Phenix, including d99 to estimate resolution, phenix.auto_sharpen to improve maps, and phenix.mtriage to analyze cryo-EM maps. We suggest that cryo-EM half-maps and masks are deposited to facilitate evaluation and validation of cryo-EM derived atomic models and maps. We also present the application of these tools to deposited cryo-EM atomic models and maps.

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New tools for the analysis and validation of Cryo-EM maps and atomic models

Four novel complexes, {[Ni4(HEIDC)4(H2O)8]·2H2O} (1), {[Mn(HEIDC)(4,4′-bipy)0.5(H2O)]·H2O}n (2), [Mn6(EIDC)4(py)(H2O)4]n (3), and {[Cd2(EIDC)(H2EIDC)(4,4′-bipy)1.5]·H2O}n (4) (H3EIDC = 2-ethyl-1H-imidazole-4,5-dicarboxylic acid, 4,4′-bipy = 4,4′-bipyridine, and py = pyridine) have been hydro(solvo)thermally synthesized by fine control over synthetic conditions, such as solvent and pH value, and structurally characterized. It is shown through single-crystal X-ray diffractions that the ligands H3EIDC can be either singly, doubly, or triply deprotonated and can coordinate to Ni(II), Mn(II) or Cd(II) ions in μ2 or μ3 modes. Compound 1 is a zero-dimensional (0D) symmetrical tetranuclear molecular square. Compound 2 exhibits a two-dimensional (2D) sheet, in which alternate left- and right-handed helical chains are bridged by 4,4′-bipy linkages. Compound 3 assumes a 2D honeycomb-like sheet built up from μ3-EIDC3− and Mn(II) atoms. Compound 4 possesses a novel three-dimensional (3D) structure constructed from 2D ...

Four novel frameworks built by imidazole-based dicarboxylate ligands: hydro(solvo)thermal synthesis, crystal structures, and properties.

Conformational analysis of furanoside-containing mono- and oligosaccharides.

Two new metal–organic frameworks [Cd3(H2O)2(C5N2O4H)2·H2O] 1 and [KCd(C7N2O4H5)] 2 have been hydrothermally synthesized employing 4,5-imidazoledicarboxylic acid (IMDC) and 2-ethyl-4,5-imidazoledicarboxylic acid (2-EtIMDC) as organic ligands. The single-crystal structure analysis reveals that compound 1 exhibits a 3-D framework, which is generated from 2-D layers pillared by 1-D chains along the c-axis. Compound 2 presents a 3-D structure with 1-D channels, which are connected in a cross-like fashion by [CdN2O3] trigonal bipyramid units and 2-EtIMDC ligands.

Assembly of two 3-D metal–organic frameworks from Cd(II) and 4,5-imidazoledicarboxylic acid or 2-ethyl-4,5-imidazoledicarboxylic acid

In the title compound, [Cd(C6H7N2O5)2], the Cd atom lies on an inversion center and has a slightly distorted octa­hedral geometry. The equatorial plane contains two bidentate 5-carb­oxy-2-methyl-1H-imidazole-4-carboxyl­ate monoanionic ligands. Two coordinated water mol­ecules occupy the axial sites. Inter­molecular N—H⋯O hydrogen bonds link the mol­ecules into chains, which are further connected by inter­molecular O—H⋯O hydrogen bonds, resulting in a three-dimensional supra­molecular framework.

Diaqua­bis(5-carb­oxy-2-methyl-1H-imid­azole-4-carboxyl­ato-κ2N3,O4)cadmium(II)

First examples of ternary lanthanide 5-aminoisophthalate complexes: Hydrothermal syntheses and structures of lanthanide coordination polymers with 5-aminoisophthalate and oxalate

The Co atom in the title compound, [Co(C6H5N2O4)2(H2O)2], is located on an inversion centre and exhibits a distorted octa­hedral geometry It is trans coordinated by two N,O-bidentate 5-carb­oxy-2-methyl-1H-imidazole-4-carboxyl­ate monoanionic ligands with two water mol­ecules in the axial positions Each ligand is stabilized by a strong, almost symmetrical, hydrogen bond Inter­molecular N—H⋯O hydrogen bonds link the mol­ecules into layers, which are further linked into a three-dimensional supra­molecular framework through O—H⋯O hydrogen-bonding inter­actions involving the water mol­ecules

Diaquabis(5‐carboxy‐2‐methyl‐1H‐imidazole‐4‐carboxylato‐κ2N3,O4)cobalt(II)

3-Hydroxy-4-oxo-2-phenyl-4H-chromene-6-carboxylic acid dimethylformamide solvate

The structure of the title compound, [Cu2Cl2(C10H8N2)]n, consists of a two-dimensional layer. Each Cl atom bridges three Cu atoms to form a ladder-like structure, whereas the 4,4′-bipyridine ligands form a link between Cu atoms of adjacent ladders, thus building a two-dimensional layer structure.

Chong-Bo Liu

Papers

Diaquabis(5-carboxy-2-methyl-1H-imidazole-4-carboxylato-κ2N3,O4)cadmium(II)

First examples of ternary lanthanide 5-aminoisophthalate complexes: Hydrothermal syntheses and structures of lanthanide coordination polymers with 5-aminoisophthalate and oxalate

Diaquabis(5‐carboxy‐2‐methyl‐1H‐imidazole‐4‐carboxylato‐κ2N3,O4)cobalt(II)

3-Hydroxy-4-oxo-2-phenyl-4H-chromene-6-carboxylic acid dimethylformamide solvate

Poly[di-μ3-chloro-μ2-4,4′-bipyridine-dicopper(I)]

Chong-Bo Liu

Papers

Diaqua­bis(5-carb­oxy-2-methyl-1H-imid­azole-4-carboxyl­ato-κ2N3,O4)cadmium(II)

First examples of ternary lanthanide 5-aminoisophthalate complexes: Hydrothermal syntheses and structures of lanthanide coordination polymers with 5-aminoisophthalate and oxalate

Diaquabis(5‐carboxy‐2‐methyl‐1H‐imidazole‐4‐carboxylato‐κ2N3,O4)cobalt(II)

3-Hydroxy-4-oxo-2-phenyl-4H-chromene-6-carboxylic acid dimethylformamide solvate

Poly[di-μ3-chloro-μ2-4,4′-bipyridine-dicopper(I)]

Diaquabis(5-carboxy-2-methyl-1H-imidazole-4-carboxylato-κ2N3,O4)cadmium(II)