Sandobox 027 Test: Difference between revisions
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== Molecular Tour == | == Molecular Tour == | ||
<scene name='11/1121664/027_3p8_window_450_pse/1'>2026_09_24 test</scene> | <scene name='11/1121664/027_3p8_window_450_pse/1'>2026_09_24 test</scene><br> | ||
The Pyrococcus abyssi rubredoxin structure, with the mutations W4L and R5S was determined to 0.43 Å resolution and | 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 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 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 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. | ||
