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29 results for “Diamond Light Source”
Single-crystal X-ray diffractometry data for a sample of [Cu(HF₂)(pyrazine)₂]PF₆ collected on beamline I19-2 at Diamond Light Source
<p>Single-crystal X-ray diffractometry data for a sample of [Cu(HF₂)(pyrazine)₂]PF₆.</p> <p>These data were collected at Diamond Light Source, on beamline I19 (experiments hutch 2), on 2022-01-30, and are particularly useful for testing data reduction routines. They are known to produce good merging statistics and final structure refinement.</p> <p>The sample was prepared as follows:<br> Ammonium hexafluorophosphate (NH₄PF₆) (0.310 g, 1.9 mmol), ammonium hydrogen difluoride ((NH₄)HF₂) (0.109 g, 1.9 mmol) and pyrazine (C₄H₄N₂) (0.300 g, 3.7 mmol) were dissolved in 5 mL of deionised water. The obtained colourless solution was slowly added to a blue solution of copper(II) nitrate prepared by dissolving copper(II) nitrate hemipentahydrate (Cu(NO₃)₂ · 2.5(H₂O)) (0.425 g, 1.8 mmol) in 5 mL of deionised water. The solutions were mixed in a plastic beaker at room temperature. The formation of blue crystals of [Cu(HF₂)(pyrazine)₂]PF₆ on the side of the beaker started after few seconds and continued for about 24 hours during which the sealed beaker was not moved.</p> <p>The sample was measured at room temperature and the illuminating beam had a wavelength of 0.4859 Å (25.52 keV).</p> <p>Beamline I19-2 at Diamond Light Source, a four-circle κ-geometry diffractometer (see <a href="https://onlinelibrary.wiley.com/doi/10.1107/97809553602060000936">[Kern 2019]</a>) with an undulator source, is described in <a href="https://doi.org/10.1107/S0909049512008801">[Nowell 2012]</a> but has since been upgraded to use a Dectris Eiger2 X 4M CdTe hybrid photon counting detector. The data are written in the <a href="https://manual.nexusformat.org/classes/applications/NXmx.html">NXmx variant</a> of the <a href="https://www.nexusformat.org/">NeXus format</a>, and so include metadata with a functionally complete description of the diffractometer.</p> <p>Inventory of data:</p> <ul> <li><strong><code>01_CuHF2pyz2PF6b_Phi.tar.xz</code></strong><br> A single 1750-image 350° φ rotation scan from -175° to 175° with 0.2° rotation per image, an exposure time of 0.1 s per image, ω = -90°, κ = 0° and 2θ = 0°.</li> <li><strong><code>02_CuHF2pyz2PF6b_2T.tar.xz</code></strong><br> A single 1750-image 350° φ rotation scan from -175° to 175° with 0.2° rotation per image, an exposure time of 0.1 s per image, ω = -90°, κ = 0° and 2θ = 20°.</li> <li><strong><code>03_CuHF2pyz2PF6b_P_O.tar.xz</code></strong><br> Two sequential rotation scans: <ul> <li><strong><code>CuHF2pyz2PF6b_P_O_01.nxs</code></strong><br> A 1750-image 350° φ scan from -175° to 175° with ω = -90°, κ = 0° and 2θ = 0°.</li> <li><strong><code>CuHF2pyz2PF6b_P_O_02.nxs</code></strong><br> A 600-image 120° ω scan from -125° to -5° with φ = -90°, κ = 45° and 2θ = 0°.</li> </ul> Both scans had 0.2° rotation per image and an exposure time of 0.1 s per image.</li> </ul> <p>The same sample was used for all these measurements. Throughout, the sample-to-detector distance was 85 mm and the beam was attenuated to 0.2% of its full intensity.</p> <p>For each rotation scan, the data comprise a single top-level NXmx-format NeXus file named <code><filename>.nxs</code>, one or more image files named <code><filename>_00000n.h5</code>, where <code>n</code> is a numeral, and a single detector metadata file named <code><filename>_meta.h5</code>. The NeXus file contains an HDF5 virtual data set that links to the data in the image file(s), and several HDF5 external links to data in the detector metadata file.</p> <p>For internal reference of Diamond Light Source staff, these data were collected as part of commissioning visit CM31144-1. Some file names and corresponding HDF5 link targets have been altered from their original names for consistency with the file contents.</p>
Example data set from Diamond Light Source VMXi beamline (Eiger 4M data, NeXus format)
<p>Data set recorded from Thermolysin crystal record <em>in situ</em> with Eiger 4M detector, to demonstrate file format used for this instrument at Diamond Light Source. Processing results using xia2 / DIALS:</p> <p> </p> <pre>For AUTOMATIC/DEFAULT/SAD Overall Low High High resolution limit 1.97 5.35 1.97 Low resolution limit 46.86 46.87 2.01 Completeness 59.8 73.2 6.0 Multiplicity 5.8 8.0 1.1 I/sigma 13.6 24.4 1.8 Rmerge(I) 0.072 0.050 0.308 Rmerge(I+/-) 0.067 0.048 0.000 Rmeas(I) 0.078 0.054 0.436 Rmeas(I+/-) 0.076 0.054 0.000 Rpim(I) 0.028 0.018 0.308 Rpim(I+/-) 0.035 0.023 0.000 CC half 0.997 0.998 0.450 Wilson B factor 13.401 Anomalous completeness 51.3 78.8 0.8 Anomalous multiplicity 3.3 4.8 1.0 Anomalous correlation 0.039 -0.006 0.000 Anomalous slope 0.987 dF/F 0.103 dI/s(dI) 1.086 Total observations 85069 8229 82 Total unique 14747 1031 73 Assuming spacegroup: P 6 2 2 Other likely alternatives are: P 61 2 2 P 65 2 2 P 62 2 2 P 64 2 2 P 63 2 2 Unit cell (with estimated std devs): 93.7184(3) 93.7184(3) 130.864(2) 90.0 90.0 120.0 </pre> <p> </p>
Cows, Pigs and People: Example data of cubic insulin from three different species recorded on Diamond Light Source I24
<p>Data collected at 100K on 10th May 2024 at I24 (Diamond Light Source) to investigate automatic grouping of datasets containing very subtle differences. Crystals grown by Cicely Tam following standard techniques with coordination from Felicity Bertram. For each of bovine, porcine, and human insulin, 10 degree wedges are included. Insulin from these three sources differ by 1-3 amino acids, but are otherwise structurally isomorphous. </p> <p>The purpose of the data upload is to make data available for tutorials using the DIALS toolchain (see e.g. examples at https://github.com/graeme-winter/dials_tutorials) however data are available for all purposes without limitation. </p> <p>Key:</p> <p>CIX - bovine insulin</p> <p>PIX - porcine insulin</p> <p>X - human insulin</p>
Single-crystal X-ray diffractometry data for a sample of NiCl₂-dppe collected on beamline I19-2 at Diamond Light Source
<p>Single-crystal X-ray diffractometry data for a sample of [1,2-Bis(diphenylphosphino)ethane]dichloronickel(II) (NiCl<sub>2</sub>-dppe, [(C<sub>6</sub>H<sub>5</sub>)<sub>2</sub>PCH<sub>2</sub>CH<sub>2</sub>P(C<sub>6</sub>H<sub>5</sub>)<sub>2</sub>]NiCl<sub>2</sub>).</p> <p>Data collected at Diamond Light Source I19-2 on 2015-05-18, publicly available for users to test data reduction routines. Data are known to produce good merging statistics and final refinements.</p> <p>The sample was prepared as follows:<br> Nickel chloride (II) hexahydrate (1 g, 2 mmol) was heated under vacuum to produce anhydrous nickel chloride (II) with a visible colour change from green to yellow. The resulting solid was taken up in ethanol (5 ml) and added to 1,2-bis(dimethylphosphine)ethane (dppe) (0.837 g, 2 mmol) in ethanol (10 ml). The solution was refluxed for 3 hour after which the solvent was evaporated. The small red crystals were purified by recrystallisation in acetone (70% yield).</p> <p>The sample was held at an approximate temperature of 150 K and the illuminating beam had a wavelength of 0.68890 Å (17.997 keV). The detector was held at 2θ = 25° throughout.</p> <p>Inventory of data:<br> <strong>010_Ni_dppe_Cl_2_150K01</strong> — 130° ω scan, 0.4° images, 0.4s per image, 325 images; κ = 45°, φ = 160°.<br> <strong>010_Ni_dppe_Cl_2_150K02</strong> — 130° ω scan, 0.4° images, 0.4s per image, 325 images; κ = 45°, φ = 40°.<br> <strong>010_Ni_dppe_Cl_2_150K03</strong> — 130° ω scan, 0.4° images, 0.4s per image, 325 images; κ = 45°, φ = -80°.<br> <strong>010_Ni_dppe_Cl_2_150K04</strong> — 198° ω scan, 0.4° images, 0.4s per image, 495 images; κ = 0°, φ = -80°.</p>
Tutorial Dataset from the I22 beamline at Diamond Light Source
<p>A tutorial dataset generated by the I22 beamline at Diamond Light Source to accompany the I22 beamline data reduction and analysis manual.</p>
In-situ data recorded from thaumatin crystals on Diamond Light Source VMXi
<p>Data collected as part of routine beamline commissioning, from samples of thaumatin grown in 0.1 M Sodium citrate, 0.75M Sodium / Potassium tartrate. Data were collected in unattended mode with positions identified <em>via</em> SynchWeb from photographs taken with a Formulatrix imaging system (picture included.) Each data set consists of 200 images taken with an Eiger 2X 4M detector at a distance of 186mm, with exposure time of 2 ms, wavelength 0.97950 angstroms and 2% transmission with a DMM beam. Automated processing combined data using the xia2 multiplex tool to give a sufficiently complete data set for structure solution and refinement.</p>
Multicrystal data of proteinase K collected on the VMXi beamline at the Diamond Light Source, UK
<p>These are a series of datasets which have been collected on the VMXi beamline at the Diamond Light Source, UK. They were collected <em>in-situ</em> at room temperature using a Dectris 2X 4M detector. The datasets were collected in unattended mode using samples preselected using the SynchWeb interface to ISPyB. Each dataset is a 60 degree wedge of data, collected using 1% DMM (double multilayer monochromator) beam (at a wavelength of 0.979A) with an exposure time of 0.002 secs/ frame. These data were merged and have been used in the deposition of a structure to the protein databank.</p>
EI STFC Power of Light animation - introducing Big Questions and Diamond Light Source
<p>The ‘Power of Light’ project brings together research scientists, higher institution educators and research fellows, teachers, and STEM ambassadors to co-create engaging and accessible resources. The Power of Light project creates opportunities for classrooms and community settings to investigate examples of scientists’ current innovative research that is taking place in UK’s national synchrotron science facility at Diamond Light Source. </p> <p>This co-created animation identifies examples of Big Questions, introduces the synchrotron, and the value of exploring very small elements in our world to inform our thikning about Big Questions. During pilot sessions in both classroom and community settings, the animation has been successfully engaging curious minds and introducing areas of scientific research that can be explored further through the Power of Light 'zines'. This resource encourages a dialogue about the value of working in multidisciplinary ways to build and use knowledge in epistemically insightful ways.</p> <p>The particle accelerator at Diamond enables scientists to investigate the complexity of relationships in the structures of ‘things’ by investigating how atoms behave. The scientists we have been working with explain that they enter an area of research with a defined question that scientific methods and the facilities at Diamond can help them investigate. During their scientific research into a precise question further, and often unexpected, lines of enquiry can be disclosed. The Power of Light project confirms that learning about science (and how building scientific knowledge ‘works’) takes us on a journey of discovery about being human and the nature of the world around us.</p>
Thaumatin / Diamond Light Source I04 user training
<p>Data recorded on Diamond Beamline I04 as part of user training (block allocation group training; 2013-07-03) from thaumatin crystal prepared following standard methods. Data collection strategy based on recording three images and running EDNA MXv1, parameters recorded in the image header as follows at end of message.</p> <p> </p> <p>Objective of publishing data: (i) testing system (ii) making tutorial data available for DIALS project (http://dials.sourceforge.net) (iii) illustrating methods for publishing raw data for MX community.</p> <p> </p> <p># Detector: PILATUS 6M Prosport+, S/N 60-0100 Diamond</p> <p># 2013-07-03T09:49:57.347</p> <p># Pixel_size 172e-6 m x 172e-6 m</p> <p># Silicon sensor, thickness 0.000320 m</p> <p># Exposure_time 0.0645000 s</p> <p># Exposure_period 0.0670000 s</p> <p># Tau = 199.1e-09 s</p> <p># Count_cutoff 161977 counts</p> <p># Threshold_setting: 6329 eV</p> <p># Gain_setting: mid gain (vrf = -0.200)</p> <p># N_excluded_pixels = 1629</p> <p># Excluded_pixels: badpix_mask.tif</p> <p># Flat_field: (nil)</p> <p># Trim_file: p6m0100_E12658_T6329_vrf_m0p20.bin</p> <p># Image_path: /ramdisk/2013/mx4014-3/20130703/thaumatin/</p> <p># Comment: Mini kappa in use</p> <p># Wavelength 0.97625 A</p> <p># Energy_range (0, 0) eV</p> <p># Detector_distance 0.26527 m</p> <p># Detector_Voffset 0.00000 m</p> <p># Beam_xy (1225.35, 1193.47) pixels</p> <p># Filter_transmission 0.2498</p> <p># Start_angle 82.0000 deg.</p> <p># Angle_increment 0.1500 deg.</p> <p># Detector_2theta 0.0000 deg.</p> <p># Polarization 0.990</p> <p># Alpha 0.0000 deg.</p> <p># Kappa 0.0000 deg.</p> <p># Phi 0.0000 deg.</p> <p># Phi_increment 0.0000 deg.</p> <p># Omega 82.0000 deg.</p> <p># Omega_increment 0.1500 deg.</p> <p># Chi 0.0000 deg.</p> <p># Chi_increment 0.0000 deg.</p> <p># Oscillation_axis X, CW</p> <p># N_oscillations 1</p> <p> </p>
Example Cytidine data set from I19-1 at Diamond Light Source
<p>Data set recorded in 6 scans, three omega and three phi, on the updated Diamond Light Source beamline I19-1, as part of routine commissioning. These data have been processed several times with different packages and are being made available to the community as an example set to allow other data processing software authors to verify the content of the data and headers.</p>
Low dose, high multiplicity thermolysin X-ray diffraction data from Diamond Light Source beamline I03
<p>Low dose, high multiplicity X-ray diffraction data recorded from a thermolysin crystal prepared according to standard protocols as part of ongoing research. The data were recorded with low transmission to ensure minimal radiation damage, with the side-effect that the individual reflections are exceedingly weak even at low resolution, and the majority of background pixels have no counts.</p>
NiDPPE data recorded as part of beamline commissioning at Diamond Light Source I19-1
<p>This is an example data set recorded as part of beamline commissioning, consisting of a 360-degree phi scan with two-theta = 0 followed by three 170-degree omega scans with phi = 0, 120, 240 with two-theta offset to 30-degrees. Data recorded with a Pilatus 2M detector with 320um sensor, so the detector sensitivity needs to be considered carefully. Automatic processing using xia2 & DIALS gives:</p> <blockquote> <p>High resolution limit 0.65 3.56 0.65<br /> Low resolution limit 11.33 11.33 0.66<br /> Completeness 98.2 99.1 69.8<br /> Multiplicity 6.1 12.9 1.6<br /> I/sigma 12.0 71.2 0.9<br /> Rmerge 0.044 0.021 0.490<br /> Rmeas(I) 0.047 0.022 0.674<br /> Rmeas(I+/-) 0.047 0.022 0.674<br /> Rpim(I) 0.016 0.006 0.460<br /> Rpim(I+/-) 0.016 0.006 0.460<br /> CC half 1.000 1.000 0.732<br /> Total observations 57622 890 547<br /> Total unique 9400 69 332<br /> Assuming spacegroup: P 1 21/n 1<br /> Unit cell:<br /> 9.417 17.109 15.392<br /> 90.000 100.851 90.000</p> </blockquote>
L Cysteine Data collected 05/03/2016 at Diamond Light Source I19-1
<p>Data collected 05/03/2016 at Diamond Light Source I19-1 publicly available for users to test data reduction routines. Data are known to produce good merging statistics and final refinements. Three datasets collected on the same crystal with varying data collection times to explore beamline operational efficiency.</p> <p>l-cyst - collected with default set of runs that i19 used in the initial phase (i.e. 0.1 degree images, 0.1s per image)</p> <p>l-cyst_fast - collected with 0.1 degree images, 0.05s per image.</p> <p>l-cyst_very_fast - collected with 0.2 degree images, 0.05s per image.</p>
Example data from a grid scan of a thaumatin crystal recorded at Diamond Light Source beamline I03
<p>Example data recorded at Diamond Light Source beamline I03 as part of ongoing methods development. This is published to allow software authors to benchmark their analysis. Data were recorded with Pilatus3 6M detector as follows:</p> <p># 2016-04-27T10:02:44.731<br /> # Pixel_size 172e-6 m x 172e-6 m<br /> # Silicon sensor, thickness 0.001000 m<br /> # Exposure_time 0.0990000 s<br /> # Exposure_period 0.1000000 s<br /> # Tau = 0 s<br /> # Count_cutoff 1009797 counts<br /> # Threshold_setting: 6350 eV<br /> # Gain_setting: autog (vrf = 1.000)<br /> # N_excluded_pixels = 1161<br /> # Excluded_pixels: badpixel_mask.tif<br /> # Flat_field: FF_p60-0126_E12700_T6350_vrf_m0p100.tif<br /> # Trim_file: p60-0126_E12700_T6350.bin<br /> # Image_path: /ramdisk/2016/cm14451-2/20160427/gw/grid-test/0002/<br /> # Ratecorr_lut_directory: ContinuousStandard_v1.1<br /> # Retrigger_mode: 1<br /> # Wavelength 0.97625 A<br /> # Energy_range (0, 0) eV<br /> # Detector_distance 0.33810 m<br /> # Detector_Voffset 0.00000 m<br /> # Beam_xy (1246.42, 1208.60) pixels<br /> # Flux 0.000000<br /> # Filter_transmission 0.0100<br /> # Start_angle -0.0002 deg.<br /> # Angle_increment 0.0000 deg.<br /> # Detector_2theta 0.0000 deg.<br /> # Polarization 0.990<br /> # Alpha 0.0000 deg.<br /> # Kappa 0.0000 deg.<br /> # Phi 0.0000 deg.<br /> # Phi_increment 0.0000 deg.<br /> # Omega -0.0002 deg.<br /> # Omega_increment 0.0000 deg.<br /> # Chi 0.0000 deg.<br /> # Chi_increment 0.0000 deg.<br /> # Oscillation_axis X.CW<br /> # N_oscillations 1</p> <p> </p>
Beta-Lactamase X-ray diffraction data recorded at Diamond Light Source I04 as part of commissioning & development
<p>X-ray diffraction data from crystals of beta-lactamase recorded during commissioning. The data were recorded in two omega scans of 3600 images @ 0.1 degrees / frame with different kappa and phi settings on a mini kappa device, with a Dectris PILATUS2 6M detector, at a wavelength of 1.239850A (10keV) for remote-SAD on the native Zn site.</p> <p> </p> <p>Data uploaded for education and tutorial purposes as a good quality example set using multi-axis geometry. </p> <p> </p> <p>For convenience the data are compressed with gzip and combined into one tar file for each sweep.</p>
45° dataset from cubic insulin recorded at the I23 beamline of Diamond Light Source
<p>450 miniCBF X-ray diffraction images from a 45° rotation scan of a cubic insulin crystal recorded at the I23 beamline of Diamond Light Source as part of commissioning tests.</p> <p>This dataset is provided as a small, but complete, diffraction dataset from I23, which has the unique DECTRIS P12M detector. A simple script for processing the data using DIALS 3.10 is as follows:</p> <pre><code class="language-bash">dials.import first450/data_1_*.cbf\ fast_slow_beam_centre=1080,57,12 dials.find_spots imported.expt d_max=75 dials.index imported.expt strong.refl dials.refine indexed.{expt,refl} dials.integrate refined.{expt,refl} dials.symmetry integrated.{expt,refl} dials.scale symmetrized.{expt,refl} </code></pre> <p>The initial beam centre read from the image headers is not correct, so the corrected value is enforced on input in the above script.</p>
Multicrystal dataset of Lysozyme, collected at room temperature, using a multilayer monochromator on beamline VMXi, Diamond Light Source
<p>21 lysozyme crystals had 10 degrees of x-ray diffraction data collected on them and all data were automatically scaled and merged using xia2.multiplex. This file is the resultant dataset.</p>
0.48 Angstrom 3,5-dinitrobenzoic acid (3,5-DNBA) C2/c polymorph single crystal X-ray diffraction data set recorded at Diamond Light Source I19-1
<p>Data set from 3,5-dinitrobenzoic acid (3,5-DNBA) C2/c polymorph recorded during in house research (DLS proposal: NR18193). Each run is saved as a single compressed tar file for convenience, runs 1, 2, 3 correspond to 3 x 170 degree omega scans at phi 0, 120, 240 degrees with 2-theta of 30 degrees, run 4 phi scan at 2-theta 0, runs 5-8 omega scans at 2-theta 55 degrees, giving data to 0.48A.</p> <p> </p> <p>Now including scale factor graph & report from processing</p>
Updated example thaumatin data set from Diamond Light Source VMXi
<p>Example data set from the VMXi beamline at Diamond Light Source recorded in situ from a thaumatin crystal with processing results:</p> <p> </p> <pre>For AUTOMATIC/DEFAULT/NATIVE Overall Low High High resolution limit 1.85 5.02 1.85 Low resolution limit 50.49 50.50 1.88 Completeness 68.0 100.0 2.7 Multiplicity 3.3 3.9 1.0 I/sigma 12.9 24.8 1.4 Rmerge(I) 0.056 0.031 0.386 Rmerge(I+/-) 0.047 0.027 0.000 Rmeas(I) 0.065 0.035 0.545 Rmeas(I+/-) 0.061 0.035 0.000 Rpim(I) 0.032 0.017 0.386 Rpim(I+/-) 0.038 0.022 0.000 CC half 0.998 0.999 0.000 Wilson B factor 20.100 Anomalous completeness 58.0 99.8 0.1 Anomalous multiplicity 1.9 2.4 1.0 Anomalous correlation -0.015 -0.107 0.000 Anomalous slope 0.928 Total observations 53105 5240 32 Total unique 15898 1349 31 Assuming spacegroup: P 41 21 2 Other likely alternatives are: P 43 21 2 Unit cell (with estimated std devs): 58.6330(3) 58.6330(3) 151.4573(10) 90.0 90.0 90.0 </pre>
Small example Eiger 2X 16M data set from Diamond Light Source I04
<p>Useful small (488 frame) Eiger data set recorded during routine testing, useful for software testing as it is small. Data recorded from a thaumatin crystal (unfortunate naming on my part) </p> <p> </p> <p>Revision includes screening images, and addition of name dataset in /entry/instrument</p> <p> </p> <pre>> h5dump -d /entry/instrument/name Therm_6_2.nxs HDF5 "Therm_6_2.nxs" { DATASET "/entry/instrument/name" { DATATYPE H5T_STRING { STRSIZE H5T_VARIABLE; STRPAD H5T_STR_NULLTERM; CSET H5T_CSET_ASCII; CTYPE H5T_C_S1; } DATASPACE SCALAR DATA { (0): "Macromolecular Crystallography I04" } } } </pre>
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