R axis 4 detector

Manufactured by Rigaku

Sourced in Japan

The R-AXIS IV++ detector is a high-performance imaging plate detector manufactured by Rigaku. It is designed for use in X-ray diffraction applications, providing efficient detection of X-ray signals. The detector employs imaging plate technology, which offers a wide dynamic range and high spatial resolution for accurate data collection.

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Lab products found in correlation

Micromax 007hf, by Rigaku (5 mentions) Ru h3r, by Rigaku (1 mentions) Structure studio, by Rigaku (1 mentions) Micromax 007 generator, by Rigaku (1 mentions) Varimax hr optics, by Rigaku (1 mentions) Pilatus 6m detector, by Dectris (1 mentions) Micromax 007, by Rigaku (1 mentions) 1.2 kw mmx007 generator, by Rigaku (1 mentions)

15 protocols using r axis 4 detector

High-Pressure Powder XRD and Mössbauer Spectroscopy

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Paper hydrostatic condition. High-pressure powder patterns were recorded on an imaging plate (Rigaku, R-AXIS IV++) detector. The data were converted into one-dimensional profiles (2θintensity data) using IP Analyzer software. 25 The XRD profiles were analysed using PDIndexer. 25 Pressures were determined by the ruby fluorescence method. 26 Measurements were performed at rt in compression up to ca. 5 GPa.
57 Fe Mössbauer spectroscopy 57 Fe Mössbauer spectra of 2 and 3 were recorded at 70 K and 200 K on a constant acceleration spectrometer with a γ-ray source of 57 Co/Rh in the transmission mode. Measurements were performed using a closed-cycle helium refrigerator (Iwatani Industrial Gases Corp.) and a conventional Mössbauer spectrometer (Topologic Systems). All isomer shifts were obtained relative to α-Fe at rt. The Mössbauer spectra were fitted using the least-squares fitting program MossWinn 4.0. 27

Taniai R., Endo T., Kanetomo T., Okazawa A., Kadobayashi H., Kawaguchi S.I, & Enomoto M. (2023). ⁵⁷Fe Mössbauer spectroscopy and high-pressure structural analysis for the mechanism of pressure-induced unique magnetic behaviour in (cation)[Fe^IIFe^III(dto)₃] (cation = Ph₄P and ⁿPrPh₃P; dto = 1,2-dithiooxalato). Dalton transactions (Cambridge, England : 2003), 52(24).

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X-ray Diffraction Analysis of GH Fibrils

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For X-ray diffraction studies, GH fibrils were isolated as mentioned in the previous section and were loaded into a clean pre-dried 0.7 mm capillary tube. Then the sample in glass capillary tube was allowed to dry for 1–2 days under vacuum. The entire capillary with dried protein film was mounted in the path of X-ray beam. The dried sample was placed in x-ray beam at 1.2 kW for 5 min exposure. The images were obtained using Rigaku R Axis IV++ detector (Rigaku, Japan) mounted on a rotating anode. The sample to detector distance was kept 300 mm and the image files were analyzed using Adxv software.

Jacob R.S., Das S., Ghosh S., Anoop A., Jha N.N., Khan T., Singru P., Kumar A, & Maji S.K. (2016). Amyloid formation of growth hormone in presence of zinc: Relevance to its storage in secretory granules. Scientific Reports, 6, 23370.

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Fvan-cmp Protein Crystal Structure

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Data were collected on the home-source diffractometer at the University of Waterloo using a Rigaku RUH3R rotating-anode generator and a Rigaku R-AXIS IV⁺⁺ detector. Data collection took place at a temperature of 93 K and a wavelength of 1.54 Å. Diffraction data were processed with Structure Studio and HKL-2000 (Otwinowski & Minor, 1997 ▸ ). Fvan-cmp protein crystals diffracted to a resolution of 2.2 Å and appeared to belong to space group P2₁2₁2₁. The asymmetric unit contained one molecule. There was no evidence of oligomerization in solution or in the crystal. Data-collection statistics are reported in Table 1 ▸.

Dowling N.V., Naumann T.A., Price N.P, & Rose D.R. (2023). Crystal structure of a polyglycine hydrolase determined using a RoseTTAFold model. Acta Crystallographica. Section D, Structural Biology, 79(Pt 2), 168-176.

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X-ray Crystallographic Analysis of PurL Mutants

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Crystals for the mutants AS-1, AS-2, ∆1, and ∆2 were obtained by hanging drop vapor diffusion method at 298 K in 2 M (NH₄)₂SO₄. Datasets for the mutant AS-1, ∆1, and ∆2 were collected at the home source of Indian Institute of Technology (IIT) Bombay using a Rigaku MicroMax-007HF x-ray diffractometer with a Rigaku R-AXIS IV++ detector. Frames were indexed, integrated, and scaled in P6₅ space group in HKL2000 (40 ). Crystal of the mutant AS-2 was diffracted at beamline ID29 using a PILATUS detector at the European Synchrotron Radiation Facility, Grenoble, France. Datasets were indexed, integrated, and scaled in P6₅ space group in XDS (41 (link)). Phases were generated, and structures were determined by performing molecular replacement in Phaser (42 (link)) and Auto-Rickshaw (43 (link)) against the published structure of native PurL (PDB ID 1T3T). Structure models were subjected to rigid body refinement and further refined using several cycles in REFMAC5 (44 (link)) in CCP4i suite (45 (link)). Manual model building was performed with WinCoot (46 (link)). Crystallographic data statistics are reported in table S2.

Sharma N., Ahalawat N., Sandhu P., Strauss E., Mondal J, & Anand R. (2020). Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation. Science Advances, 6(14), eaay7919.

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X-ray Diffraction of Ligand Complex

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X-ray diffraction experiments were performed at the home source of Indian Institute of Technology (IIT) Bombay using a Rigaku MicroMax-007HF X-ray diffractometer. A single crystal of the ligand complex was cryo-protected with 20% (v/v) ethylene glycol (prepared using mother liquor) prior to data collection. The crystal was then flash cooled in liquid nitrogen and transferred to a stream of nitrogen gas at 100K. X-ray data were collected at a wavelength of 1.5418 Å on a Rigaku R-AXIS IV++ detector. The dataset was indexed, integrated, and scaled with XDS (61 (link)). Data collection statistics are summarized in Table 1.

Singh J., Sahil M., Ray S., Dcosta C., Panjikar S., Krishnamoorthy G., Mondal J, & Anand R. (2022). Phenol sensing in nature is modulated via a conformational switch governed by dynamic allostery. The Journal of Biological Chemistry, 298(10), 102399.

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Structural Analysis of XTX100-Fab Peptide Complex

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Purified XTX100-Fab was crystallized using the hanging drop vapor diffusion method over a reservoir containing 0.5 mL of 0.2 M ammonium citrate pH 7.0 and 23% PEG 3350. Hanging drops were prepared at 60 µM XTX100-Fab with 10 x molar excess (600 µM) peptide and mixed 1:1 with reservoir solution.
Crystals were harvested in cryoprotectant (1:1 mix of 35% (w/v) meso-erythritol and reservoir solution) and mounted under cryo-conditions on a Rigaku MicroMax007-HF rotating anode diffractometer with a Rigaku RAXIS IV++ detector. A native dataset was collected at 1.5418 Å at 100 K and processed using X-ray Detector Software (XDS), resulting in a 98.8% complete dataset to 3.0 Å. The complex crystallized in space group P2₁2₁2₁ (unit cell dimensions 72.1 Å, 202.8 Å, 224.6 Å, 90°, 90°, 90°) with six complexes per asymmetric unit.
The initial solution was obtained via molecular replacement using Phaser in the Phenix suite with previously determined XTX100-Fab as a search model as a search model. This solution was then subjected to several cycles of manual building followed by refinement using phenix.refine. Data collection and refinement statistics are listed in online supplemental table 2.

Jenkins K.A., Park M., Pederzoli-Ribeil M., Eskiocak U., Johnson P., Guzman W., McLaughlin M., Moore-Lai D., O’Toole C., Liu Z., Nicholson B., Flesch V., Qiu H., Clackson T., O’Hagan R.C., Rodeck U., Karow M., O’Neil J, & Williams J.C. (2023). XTX101, a tumor-activated, Fc-enhanced anti-CTLA-4 monoclonal antibody, demonstrates tumor-growth inhibition and tumor-selective pharmacodynamics in mouse models of cancer. Journal for Immunotherapy of Cancer, 11(12), e007785.

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XTX100-Fab Protein Crystallization

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Purified XTX100-Fab was crystallized using the hanging drop vapor diffusion method over a reservoir containing 0.5 mL of 0.2 M ammonium citrate dibasic pH 5.0 with 20% PEG 3350. Hanging drops were prepared at 60 µM XTX100-Fab with 10 x molar excess (600 µM) peptide and mixed 1:1 with reservoir solution.
Crystals were harvested in cryoprotectant (1:1 mix of 35% (w/v) meso-erythritol and reservoir solution) and mounted under cryo-conditions on a Rigaku MicroMax007-HF rotating anode diffractometer with a Rigaku RAXIS IV++ detector. A native dataset was collected at 1.5418 Å at 100 K and processed using XDS, resulting in a 96.6% complete dataset to 2.4 Å resolution. The complex crystallized in space group I21 (unit cell dimensions 63.38 Å, 57.9 Å, 116.267 Å, 90°, 95.6°, 90°) with one complex per asymmetric unit.
The initial solution was obtained via molecular replacement using Phaser in the Phenix suite with previously determined XTX100-Fab as a search model. This solution was then subjected to several cycles of manual building followed by refinement using phenix.refine. Data collection and refinement statistics are listed in online supplemental table 2.

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Structural Analysis of PRL/GAL Fibrils

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PRL/GAL fibrils were isolated by ultracentrifugation as mentioned earlier and were loaded into a clean 0.7 mm capillary. The samples in capillary were dried overnight under vacuum. The whole capillary with dried protein was placed in the path of X-ray beam. The dried film of protein was placed in an X-ray beam at 200 K for 120 s exposure. The resulting images were collected using a Rigaku R-Axis IV ++ detector (Rigaku, Japan) kept on a rotating anode. The distance between the sample to the detector was 200 mm and the image files were analyzed and processed using Adxv software.

Chatterjee D., Jacob R.S., Ray S., Navalkar A., Singh N., Sengupta S., Gadhe L., Kadu P., Datta D., Paul A., Arunima S., Mehra S., Pindi C., Kumar S., Singru P., Senapati S, & Maji S.K. (2022). Co-aggregation and secondary nucleation in the life cycle of human prolactin/galanin functional amyloids. eLife, 11, e73835.

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Crystallization and Structure Determination of BcCspΔ36–37

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Crystallization conditions were initially screened using a high-throughput ARI Gryphon crystallization robot (Arts Robbins Instruments LLC, Sunnyvale, CA, USA) and the Crystal Screen HT reagent kit (Hampton Research Corp., Aliso Viejo, CA, USA). BcCspΔ36–37 crystals were obtained using the hanging drop vapor diffusion method within two weeks of equilibration at 291 K of a protein solution containing 20 mg·ml⁻¹BcCspΔ36–37 in 20 mM sodium phosphate pH 4.6 with a reservoir solution containing 0.1 M sodium acetate pH 4.6, 0.2 M ammonium sulfate, 30% v/v poly(ethylene glycol) methyl ether 2000 after mixing equal volumes of both solutions.
Complete diffraction data up to 1.8 Å were collected at 100K on a Rigaku MicroMax 007 HF X-ray generator equipped with a R-AXIS IV++ detector (Rigaku Corp., TK, Japan) using a wavelength of 1.54 Å. Data were indexed and integrated with XDS [56 (link)] and scaled with AIMLESS [57 (link)]. The crystal structure was solved by molecular replacement with PHASER [58 (link)], using the β-strands of the domain-swapped dimer of BcCsp (PDB accession number 2HAX) as a search model. The structure was refined using PHENIX [59 (link)] and COOT [60 (link)] and the final structure was validated using MOLPROBITY [61 (link)]. Data collection and refinement statistics are summarized in Table 4. All structure figures were generated using PyMol [62 ].

Carvajal A.I., Vallejos G., Komives E.A., Castro-Fernández V., Leonardo D.A., Garratt R.C., Ramírez-Sarmiento C.A, & Babul J. (2017). Unusual dimerization of a BcCsp mutant leads to reduced conformational dynamics. The FEBS journal, 284(12), 1882-1896.

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Xenon Anomalous Diffraction Protocols

Cited 2 times

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Diffraction data for
Cp1-Xe was collected remotely from the Stanford Synchrotron Radiation
Light source (SSRL) on beamline 12-2 with a DECTRIS Pilatus 6 M detector.
Reference sets of 1440 diffraction images were collected at 12999.97
eV with an oscillation angle of 0.25° over 360° rotation.
To confirm the identity of the Xe sites, diffraction data were also
collected at 6690.11 eV using the same strategy. Although well above
the L-edge, Xe exhibits significant anomalous scattering at this energy
with Δf″ ≈ 10 electrons. Diffraction
data for Av1-Xe was collected in-house on a Rigaku MicroMax 007-HF
X-ray generator with a Rigaku RAXIS-IV++ detector. All data sets were
integrated with the XDS program package.^{38 (link)} Scaling was carried out with the CCP4 suite,^{39 (link)} and phasing was determined by molecular replacement against
Av1 (PDB ID 3U7Q) and Cp1 (4WES).^{36 (link),40 (link)} Initial refinement was carried out with
CNS,^{41 (link)} and alternative conformations and
isotropic B-factors were refined with REFMAC5.^{42 (link),43 (link)} Simulated annealing was performed using PHENIX.^{44 (link)}

Morrison C.N., Hoy J.A., Zhang L., Einsle O, & Rees D.C. (2015). Substrate Pathways in the Nitrogenase MoFe Protein by Experimental Identification of Small Molecule Binding Sites. Biochemistry, 54(11), 2052-2060.

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