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

Four metal–organic frameworks, namely, [Cd2(μ2-HPhIDC)2(phen)2] (H3PhIDC = 2-phenyl-1H-imidazole-4,5-dicarboxylic acid, phen = 1,10-phenanthroline) (1), [Cd2(μ2-HPhIDC)2(2,2′-bipy)2] (2,2′-bipy = 2,2′-bipyridine) (2), [Pb3(μ4-PhIDC)2(H2O)] (3) and [Sr(μ2-H2PhIDC)2(H2O)4]·2H2O (4) have been synthesized under hydro(solvo)thermal conditions, and characterized by elemental analysis, IR spectroscopy and single crystal X-ray diffraction. Both 1 and 2 are one-dimensional (1-D) infinite chains. Compound 3 features a two-dimensional (2-D) framework, in which Pb2+ ions are bridged by μ4-PhIDC3− ligands. Compound 4 possesses a three-dimensional (3-D) framework with a uninodal 4-connected net. The thermal and photoluminescence properties of polymers 1–4 have been investigated as well.

2-Phenyl-4,5-imidazole dicarboxylate-based metal–organic frameworks assembled under hydro(solvo)thermal conditions

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)

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.

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

In sugar molecule of the title compound, C22H29Cl3O13·C7H8, the pyran­ose ring adopts the expected chair conformation. The acetoxy­methyl and two acet­oxy substituents are in the equatorial positions of this ring. In the crystal structure, there is a single weak C—H⋯O inter­molecular inter­action (H⋯O = 2.46 A), which links mol­ecules into chains in the a-axis dirextion.

6‐(Acetoxy­meth­yl)‐5‐chloro‐2‐[(2R,3R,4R,5S)‐3,4‐diacet­oxy‐2,5‐bis­(chloro­meth­yl)‐2,3,4,5‐tetra­hydro­furan‐2‐yl­oxy]‐3,4,5,6‐tetra­hydro‐2H‐pyran‐3,4‐diyl diacetate toluene solvate

In the title compound, C12H14ClN5O4, the dihedral angles between the purine plane and two methoxy­carbonyl planes are 15.806 (19) and 68.818 (18)°. Inter­molecular N—H⋯O and N—H⋯N hydrogen bonds link mol­ecules into bands along the b axis; they are further aggregated via C—H⋯O inter­actions into layers parallel to the ab plane.

Dimethyl 2‐[2‐(2‐amino‐6‐chloro­purin‐9‐yl)eth­yl]malonate

In the sugar mol­ecule of the title compound, C104H94O11·CH4O·075C4H8O, the pyran­ose ring adopts the expected chair conformation Weak intra- and inter­molecular C—H⋯O hydrogen bonds, in part, control the mol­ecular conformation and stabilize the crystal structure

2-[(2R,3S,4S,5S)-3,4-Benzyloxy-2,5-bis(trityloxymethyl)tetrahydrofuran-2-yloxy]-3,4,5-tribenzyloxy-6-(trityloxymethyl)tetrahydropyran–methanol–2-butanone (1/1/0.75)

Zi-Sheng Wu

Papers

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

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

6‐(Acetoxymethyl)‐5‐chloro‐2‐[(2R,3R,4R,5S)‐3,4‐diacetoxy‐2,5‐bis(chloromethyl)‐2,3,4,5‐tetrahydrofuran‐2‐yloxy]‐3,4,5,6‐tetrahydro‐2H‐pyran‐3,4‐diyl diacetate toluene solvate

Dimethyl 2‐[2‐(2‐amino‐6‐chloropurin‐9‐yl)ethyl]malonate

2-[(2R,3S,4S,5S)-3,4-Benzyloxy-2,5-bis(trityloxymethyl)tetrahydrofuran-2-yloxy]-3,4,5-tribenzyloxy-6-(trityloxymethyl)tetrahydropyran–methanol–2-butanone (1/1/0.75)

Zi-Sheng Wu

Papers

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

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

6‐(Acetoxy­meth­yl)‐5‐chloro‐2‐[(2R,3R,4R,5S)‐3,4‐diacet­oxy‐2,5‐bis­(chloro­meth­yl)‐2,3,4,5‐tetra­hydro­furan‐2‐yl­oxy]‐3,4,5,6‐tetra­hydro‐2H‐pyran‐3,4‐diyl diacetate toluene solvate

Dimethyl 2‐[2‐(2‐amino‐6‐chloro­purin‐9‐yl)eth­yl]malonate

2-[(2R,3S,4S,5S)-3,4-Benzyloxy-2,5-bis(trityloxymethyl)tetrahydrofuran-2-yloxy]-3,4,5-tribenzyloxy-6-(trityloxymethyl)tetrahydropyran–methanol–2-butanone (1/1/0.75)

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

6‐(Acetoxymethyl)‐5‐chloro‐2‐[(2R,3R,4R,5S)‐3,4‐diacetoxy‐2,5‐bis(chloromethyl)‐2,3,4,5‐tetrahydrofuran‐2‐yloxy]‐3,4,5,6‐tetrahydro‐2H‐pyran‐3,4‐diyl diacetate toluene solvate

Dimethyl 2‐[2‐(2‐amino‐6‐chloropurin‐9‐yl)ethyl]malonate