Sandobox 027 Test

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spinqualitylabelsall models Caption for this structure Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D This is a default text for your page Sandobox 027 Test. Click above on edit this page to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia or to the article describing Jmol to the rescue. 2026_09_24 test 027_Initl_Scene Molecular Tour 027_3p8_window_450_pse The Pyrococcus abyssi rubredoxin structure, with the mutations W4L and R5S, was determined to 0.43 Å resolution and refined using an independent atom model (IAM), PDB-ID 30or, and a transferable aspherical atom model (TAAM), PDB-ID 30oh. Several technical advances were essential to achieve this high-quality, ultra-high-resolution structure. The authors used a large, well-ordered crystal, with approximate dimensions of 600 × 500 × 300 µm, mounted in a Kapton loop and flash-cooled directly in liquid nitrogen. The dataset was collected at 100 K on the PETRA III P14 beamline at EMBL Hamburg @ DESY using a high-energy X-ray beam of 32.1 keV. The diffraction data were collected using a top-hat beam rather than a conventional focused beam. The beam was approximately 600 × 500 µm, collimated using compound refractive lenses and matched to the crystal. This allowed the entire crystal volume to be used for diffraction while minimizing background scattering from the surrounding liquid. The experiment used a high-Z detector, the DECTRIS EIGER2 CdTe 16M, which has improved detective quantum efficiency at the high X-ray energies required for sub-Ångström data collection. This detector provides a wide dynamic range and makes it possible to collect data across the full resolution range in a single experiment. Data collection was executed through the Global Phasing workflow integrated with MXCuBE on the P14 beamline. This enabled a carefully designed multi-orientation strategy that fills cusp regions in reciprocal space, avoids goniostat shadowing, and distributes multiplicity more evenly than a single-orientation dataset. The workflow also feeds instrument-specific shadow information into the automated data-processing pipeline, autoPROC, which uses XDS, AIMLESS, and STARANISO. The total dose was 500 kGy, and the resulting dataset contained ‘’‘6,545,565’’’ total reflections and ‘’‘245,905’’’ unique reflections, with an average multiplicity of ‘’‘26.6’’’. In the outermost resolution shell, the data still had a CC₁/₂ of 0.621 and I/σ(I) of 1.7, indicating that the highest-resolution measurements retained significant information. The structure of ‘‘P. abyssi’’ rubredoxin at 0.43 Å resolution is one of the highest-resolution protein structures reported to date. The study is significant because it shows that, with sufficiently high-resolution data, the electron density in a protein can be interpreted not only in terms of atomic positions but also in terms of chemical bonding and valence-electron distribution. When the structure was refined in Global Phasing’s BUSTER using the standard spherical-atom independent atom model (IAM), strong positive difference density appeared at the midpoints of C–C, C–N, and C–O bonds. This pattern is characteristic of deformation density—the redistribution of electron density associated with covalent bonding relative to a simple sum of spherical atomic densities. The key finding is that refinement using a transferable aspherical atom model (TAAM), implemented by connecting the DiSCaMB library to BUSTER, largely removes these positive features from the difference maps. This provides strong evidence that the features arise from genuine bonding-related electron-density deformation rather than simply from model error or noise. In other words, the authors did not merely observe unexplained density; they showed that a chemically more realistic scattering model accounts for it. The publication associated with PDB entries 30or and 30oh represents an important advance in biological quantum crystallography. It does not simply report another high-resolution structure; it demonstrates that several demanding experimental and computational approaches—high-energy diffraction, low-dose multi-orientation data collection, high-Z detection, automated processing, and aspherical refinement—can be combined into an integrated workflow. An important implication is that detailed electron-density studies of biological macromolecules are feasible and that such data may provide structural insight into enzyme mechanisms, redox centers, and other processes in which electronic structure is important. The Fe–S₄ cluster in rubredoxin, however, still shows residual difference density, highlighting that chemically complex metal sites may require more detailed quantum-mechanical modelling. Overall, the study suggests that advances in sub-Ångström crystallography are making increasingly detailed studies of protein electron density possible, with particular relevance to enzyme catalysis and metal-cluster chemistry. References

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