Sandobox 027 Test: Difference between revisions

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You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

<scene name='11/1121664/027_Initl_Scene/1'>027_Initl_Scene</scene>

== Molecular Tour ==

<scene name='11/1121664/027_3p8_window_450_pse/1'>~~2026_09_24 test~~</scene>~~<br>~~

<scene name='11/1121664/027_3p8_window_450_pse/2'>027_3p8_window_450_pse</scene>

The <i>Pyrococcus abyssi</i> rubredoxin structure, with the mutations W4L and R5S was determined to 0.43 Å resolution and refined for the independent atom model (IAM), PDB-ID [[30or]] and for the ransferable 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 x 500 x 300 micrometres in size, 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 allows 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 [https://www.globalphasing.com] 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 remained meaningful.

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 x 500 x 300 micrometres in size, 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 [https://www.dectris.com/en/ DECTRIS] EIGER2 CdTe 16M, which has improved detective quantum efficiency at the high X-ray energies required for sub-Ångström data collection. This detector allows 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 [https://www.globalphasing.com 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 remained meaningful.

The structure of Pyrococcus 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 using standard spherical atom models in Global Phasing´s BUSTER, the 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 rather than a simple sum of spherical atomic densities. The key finding is that refinement using a transferable aspherical atom model (TAAM) by connecting the DiSCaMB library to BUSTER removes these positive features from the difference maps, confirming that they correspond to genuine electron-density deformations rather than 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.

Sandobox 027 Test: Difference between revisions

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@@ Line 4: / Line 4: @@
 You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
+<scene name='11/1121664/Sandbox_027_Test/3'>2026_09_24 test</scene><br>
+<scene name='11/1121664/027_Initl_Scene/1'>027_Initl_Scene</scene>
 == Molecular Tour ==
-<scene name='11/1121664/027_3p8_window_450_pse/1'>2026_09_24 test</scene><br>
+<scene name='11/1121664/027_3p8_window_450_pse/2'>027_3p8_window_450_pse</scene>
 The <i>Pyrococcus abyssi</i> rubredoxin structure, with the mutations W4L and R5S was determined to 0.43 Å resolution and refined for the independent atom model (IAM), PDB-ID [[30or]] and for the ransferable 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 x 500 x 300 micrometres in size, 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 allows 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 [https://www.globalphasing.com] 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 remained meaningful.
+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 x 500 x 300 micrometres in size, 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 [https://www.dectris.com/en/ DECTRIS] EIGER2 CdTe 16M, which has improved detective quantum efficiency at the high X-ray energies required for sub-Ångström data collection. This detector allows 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 [https://www.globalphasing.com 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 remained meaningful.
 The structure of Pyrococcus 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 using standard spherical atom models in Global Phasing´s BUSTER, the 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 rather than a simple sum of spherical atomic densities. The key finding is that refinement using a transferable aspherical atom model (TAAM) by connecting the DiSCaMB library to BUSTER removes these positive features from the difference maps, confirming that they correspond to genuine electron-density deformations rather than 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.