10-(4-Methylbenzylidene)anthracen-9(10<i>H</i>)-one

The MolProbity web service provides macromolecular model validation to help correct local errors, for the structural biology community worldwide. Here we highlight new validation features, and also describe how we are fighting back against recent outside changes that degrade or endanger that mission. Sophisticated hacking of the MolProbity server has required continual monitoring and various security measures short of restricting user access. Refinement software now increasingly restrains validation criteria in order to supplement the sparser experimental data at 3-4Å resolutions typical of modern cryoEM. But unfortunately the broad density allows optimization without fixing underlying problems, which means these structures often score much better than they really are. CaBLAM, our first new tool designed for this regime, was described in the previous Tools issue, and here we demonstrate its effectiveness in diagnosing local errors even when other validation outliers have been artificially removed. The deprecation of Java applets now prevents KiNG interactive online display of outliers on the 3D model during a MolProbity run, but that important functionality is now recaptured with a modified version of the Javascript NGL Viewer. Other new changes are more straightforwardly good. We are moving to the Neo4j database (graphical rather than relational), and will soon have cleaner as well as much larger reference datasets. In addition to several minor new features, we have developed a tool called UnDowser that analyzes the properties and context of modeled but clashing HOH "waters" to diagnose what they might actually represent. A dozen distinct scenarios are illustrated and described.

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X-ray crystal structure analysis of 5-bromospiro[indoline-3,7'-pyrano[3,2-C:5,6-C']dichromene]-2,6',8'-trione

Sharma

Banerjee

Kaur

et al. 2021

Eur J Chem

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An analog of spirooxindole[pyrano-bis-2H-l-benzopyran] derivatives namely 5-bromospiro [indoline-3,7'-pyrano[3,2-c:5,6-c']dichromene]-2,6',8'-trione was synthesized via one-pot pseudo three-component reaction of one equivalent of 5-bromoisatin and two equivalents of 4-hydroxycoumarin using mandelic acid as a naturally occurring organo catalyst in aqueous ethanol under reflux conditions. The synthesized compound was characterized by FT-IR, 1H NMR, 13C NMR, and HRMS data. Crystal structure was determined by using single X-ray crystallography technique. It was found that the crystals are triclinic with space group P-1, C108H60Br4N4O29S2: a = 11.8333(6) Å, b = 12.8151(6) Å, c = 17.1798(8) Å, α = 77.317(4)°, β = 74.147(4)°, γ = 66.493(5)°, V = 2280.0(2) Å3, Z = 1, T = 149.99(10) K, μ(MoKα) = 1.902 mm-1, Dcalc = 1.647 g/cm3, 11545 reflections measured (3.836° ≤ 2Θ ≤ 50.998°), 8310 unique (Rint = 0.0488, Rsigma = 0.0875) which were used in all calculations. The final R1 was 0.0622 (I > 2σ(I)) and wR2 was 0.1994 (all data). The crystal structure was solved by direct methods and refined by full-matrix least-squares procedure to a final R-value of 0.0622 for 6264 observed reflections. The crystal structure was stabilized by an elaborate system of N-H···O, O-H···O, C-H···π, and π···π interactions involving solvent molecules to form supramolecular structure.

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10-(4-Methylbenzylidene)anthracen-9(10H)-one

Cited by 4 publications

References 9 publications

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

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

CaBLAM for chiropraxis in cryoEM, UnDowser to rethink “waters”, and NGL Viewer to recapture online 3D graphics in MolProbity validation

X-ray crystal structure analysis of 5-bromospiro[indoline-3,7'-pyrano[3,2-C:5,6-C']dichromene]-2,6',8'-trione

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