SRC/FIIN-2 and SRC/TAS-120 crystal datasets were collected at the BL17U35 (link) and BL19U136 (link) beamlines of Shanghai Synchrotron Radiation Facility (SSRF), FGFR4/PRN1371 crystal data were collected using an in-house MicroMax-007 x-ray generator equipped with VariMax HR optics (Rigaku, Japan). The diffraction data were processed using HKL200037 (link). The structures were solved by molecular replacement with phaser from PHENIX package38 (link) using the previously solved SRC/Ruxolitinib structure (PDB ID: 4U5J)31 (link) as the search model for SRC/FIIN-2 and SRC/TAS-120, and FGFR4/ponatinib structure (PDB ID: 4QRC)39 (link) as the search model for FGFR4/PRN1371. The ligands were drawn by ChemDraw software and the models were building on the website http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/submit.html . Phenix.ligandfit was run to place the ligand and the correlation coefficient (CC) value was above 0.7. The best-fitting ligand was added to the structure. Then structures were refined with phenix.refine and model building was performed using WinCoot40 (link). Structural graphics were drawn by PyMOL41 . Data collection and structure refinement statistics are presented in Supplementary Table 1 .
Micromax 007
Manufactured by Rigaku
Sourced in Japan
The Rigaku MicroMax-007 is a compact and versatile X-ray diffractometer designed for a wide range of laboratory applications. It features a high-intensity microfocus X-ray source and a state-of-the-art detector, enabling high-quality data collection from small samples. The MicroMax-007 is a reliable and user-friendly instrument suitable for materials science, chemistry, and other research fields requiring detailed structural analysis.
Automatically generated - may contain errors
Lab products found in correlation
Cryostream 700 jet, by Oxford Cryosystems (2 mentions)
200k 2d area detector, by Rigaku (2 mentions)
Varimax hr optics, by Rigaku (1 mentions)
Multimode 8 instrument, by Bruker (1 mentions)
Raxis 4 imaging plate detector, by Rigaku (1 mentions)
Crystalclear, by Rigaku (1 mentions)
Morpheus, by Molecular Dimensions (1 mentions)
Crysalispro software suite, by Rigaku (1 mentions)
R axis 4, by Rigaku (1 mentions)
R axis 4 detector, by Rigaku (1 mentions)
Superdex 200 10 300 gl gel filtration chromatography, by GE Healthcare (1 mentions)
Pegs suite, by Qiagen (1 mentions)
Saturn 944, by Rigaku (1 mentions)
39 protocols using micromax 007
1
Structural Determination of Kinase Complexes
2
X-ray Crystal Structure Data Collection
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Diffraction data of the crystals obtained was collected on an in-house MAR 345dtb image plate detector, mounted on a RIGAKU MicroMax-007 HF rotating anode X-ray generator (λ = 0.15418 nm) operating at 40 kV and 30 mA. The crystal to detector distance was 200 mm. Before data collection the crystals were soaked in cryo-protectant solution containing 20% glycerol mixed with corresponding mother liquor. The temperature during data collection was maintained at 100 K using OXFORD cryostream. Total 120 frames were collected of 10 minutes each with crystal being rotated at the rate of 1°/frame. Images were scaled and merged using HKL2000 suite.
3
Structural Insights into MORF DPF-H3K14cr Complex
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Purified MORFDPF (residues 211–322) was incubated at 10 mg/ml with the H3K14cr (residues 1–19) peptide (1:1.5 molar ratio) for 1 h on ice prior crystallization in 50 mM Tris-HCl pH 7.5 buffer, supplemented with 150 mM NaCl and 1 mM dithiothreitol. Crystals of the MORFDPF-H3K14cr complex were grown using hanging-drop diffusion method at 18 °C by mixing protein-peptide solution with well solution composed of 1.1–1.3 M sodium citrate tribasic and 0.1 M sodium hepes pH 8.4–8.6 at a 1:1 ratio. The crystals were soaked in a mixture of 50% (1.1–1.3 M sodium citrate tribasic and 0.1 M sodium hepes pH 8.4–8.6) and 50−60% ethylene glycol prior to flash-freezing in liquid nitrogen. X-ray diffraction data were collected from a single crystal on the UC Denver X-ray Crystallography core facility Rigaku Micromax 007 high-frequency microfocus X-ray generator equipped with a Pilatus 200 K 2D area detector. Indexing and scaling were completed using HKL3000. The phase solution was found via molecular replacement using MORFDPF-H3K14bu structure (PDB ID 5U2J) as a model. Model building was carried out with Coot45 (link) and refinement was performed with Phenix46 (link). The final structure was validated by MOLProbity47 (link).
4
Structural Analysis of Protein Crystals
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Crystal screening and diffraction quality evaluation was mainly carried out at the in-house X-ray source and the BL17U beamline of Shanghai Synchrotron Radiation Facility (SSRF). The data set used for phasing was collected at the BL5A of Photon Factory (PF, Tsukuba, Japan) with ADSC Q315 CCD detector. The anomalous diffraction data sets of site-directed cysteine mutant crystals labelled with mercury for the verification of sequence registration on the structural model were collected on SSRF BL17U and PF BL5A/NE3A. A high-quality data set of S200C/S223C crystal used for the final structure refinement was collected at the BL1A micro-focus beamline of PF with PILATUS 2M-F detector. To minimize radiation damage, the ‘helix mode’ was applied for data collection of a total of 60° oscillation range (1°/frame) on three individual spots on the crystal to yield a complete data set. The data set of S200C/S258C mutant crystal was collected at SSRF BL17U beamline with ADSC Q315r detector. The data of BaCl2, MnCl2, TlNO3, CsCl or MnCl2+RbCl-soaked crystals were all collected with the in-house Rigaku MicroMax-007 rotating anode X-ray generator and Raxis IV detector. All data sets were collected under 100 K condition. The HKL2000 (ref. 41 ) or iMOSFLM42 (link) programmes were used for data processing.
5
Preparation and X-ray Analysis of Preformed Fibrils
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The preformed fibril samples were centrifuged at 5000g to the pellet and were washed and resuspended in 20 mM sodium phosphate buffer (pH 7.4). The samples were mixed by tapping and transferred to the 0.6 mm diameter borosilicate glass capillary (Hampton Research, UK) and sealed with clay from the narrow end. The samples were air-dried to remove excess solution to reduce noise in the XRD experiments. The data was collected using the in-house source Rigaku Micromax 007 equipped with a Mar345 detector at 1.5418 Å wavelength at room temperature. The air-dried samples were exposed for 25–30 min under the X-ray beam.
6
Structural Insights into Yaf9-H3K27ac Interaction
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Purified Yaf9-YEATS (aa 8–171) at 14 mg/ml in 20 mM Tris–HCl pH 7.5, 150 mM NaCl and 1 mM TCEP was incubated on ice with a 5 molar equivalence of H3K27ac peptide (21–31 aa) for 1–2 h. Crystals of the protein:peptide complex were grown using sitting-drop vapor diffusion against an equal volume of well solution containing 2.0 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5 at 4°C. Crystals were cryoprotected with the addition of 30% glycerol to the well solution and the X-ray diffraction data were collected on the UC Denver X-ray Crystallography core facility Rigaku Micromax 007 high-frequency microfocus X-ray generator equipped with a Pilatus 200K 2D area detector. Indexing and scaling were completed using HKL3000. The phase solution was solved with Phenix.phaser using molecular replacement and the apo- Yaf9 YEATS (PDB ID: 3FK3) structure as the model. Model building was carried out with Coot and refinement was performed with Phenix.refine (23 (link),24 (link)). The final structure was validated with MolProbity (25 (link)). Crystallographic statistics for the Yaf9 YEATS–H3K27ac structure are shown in Supplementary Table S1 .
7
Structural Determination of HIV-1 IN CCD Mutant
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The HIV-1 IN CCD (residues 50–212) containing the F185H mutation was expressed and purified as described (Sharma et al., 2014 (link)). The protein was concentrated to 8 mg/ml and crystallized using hanging-drop vapor diffusion method with a crystallization buffer consisting of 100 mM sodium cacodylate pH 6.5, 100 mM ammonium sulfate, 10% (w/v) PEG 8000, and 5 mM DTT. Crystallization drops were prepared using an equal volume of protein and well solution. Crystallization trays were prepared on ice at room temperature and then transferred to 4°C for storage. Crystals formed within one week and continued to grow thereafter in size. Crystal data were collected on a Rigaku Micromax-007 at 100 K. Data were integrated and scaled using HKL3000 (Minor et al., 2006 (link)) and Scalepack (Otwinowski and Minor, 1997 (link)). Phaser (McCoy et al., 2007 (link)) in the PHENIX suite (Adams et al., 2010 (link)) was used to run molecular replacement using Protein Data Bank code 4O55 as a search model (Sharma et al., 2014 (link)). Phenix.refine (Afonine et al., 2012 (link)) was used for data refinement, and manual refinement was done in Coot (Emsley et al., 2010 (link)). The coordinates are deposited in the Protein Data Bank under accession codes 6NUJ. The data and refinement statistics are given in Supplementary file 1 (Table S1).
8
Crystallization of Arginine-Bound TmArgBP
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Crystallization of the arginine-bound form of TmArgBP20-233_G52A was performed at 293 K by hanging-drop vapor diffusion methods. A screening/optimization of crystallization conditions was achieved using a variety of different conditions. The best crystals were obtained using a protein concentration of 6 mg ml−1 in a solution of 2.0 M ammonium sulfate as precipitating agent in a 0.1 M Tris-HCl buffer (pH 8.5).
Diffraction data were collected in-house using a Rigaku Micromax 007 HF generator, equipped with a Saturn944 CCD detector at 100 K. The data were collected by flash-cooling in the supercooled nitrogen gas produced by an Oxford Cryo-system after the addition of 10% glycerol to the harvesting solution. The crystals belonged to the C2 space group and diffracted up to 1.64 Å, although the completeness of the last shell (1.70–1.64 Å) is somehow limited (79.5%). The data set was scaled and merged using the HKL2000 program package44 (link). Statistics of data collection are reported in Table3 .
Diffraction data were collected in-house using a Rigaku Micromax 007 HF generator, equipped with a Saturn944 CCD detector at 100 K. The data were collected by flash-cooling in the supercooled nitrogen gas produced by an Oxford Cryo-system after the addition of 10% glycerol to the harvesting solution. The crystals belonged to the C2 space group and diffracted up to 1.64 Å, although the completeness of the last shell (1.70–1.64 Å) is somehow limited (79.5%). The data set was scaled and merged using the HKL2000 program package44 (link). Statistics of data collection are reported in Table
9
Structural Characterization of LCs
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The X-ray diffraction was performed with an in-house X-ray facility. X-rays were produced using a Rigaku MicroMax 007 micro-focus copper rotating anode generator running at 40kV, 20 mA and focussed onto the crystal using confocal multilayer optics. The temperature was controlled by an Oxford Cryosystems Cryostream 700 jet. Data were accumulated using a MarResearch MAR345 image plate detector system. Microscopy Observation. Tapping mode AFM imaging was performed at r.t on a Bruker Multimode 8 instrument with Nanoscope V controller. An Olympus BX-50 transmitted-light polarizing microscope equipped with a Mettler FP82 hotstage and a Coolsnap-Pro digital camera was used to observe the texture of the LCs.
10
X-ray Diffraction Analysis of PHCP Crystal Structure
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The X‐ray diffraction experiment on a PHCP crystal was carried out on a Rigaku Micromax‐007 rotating anode X‐ray generator with a Cu target equipped with an R‐AXIS IV++ imaging plate detector (Rigaku, Japan). The crystal was flash‐cooled at −173°C in a stream of cold nitrogen, using following the cryoprotectant solution: 0.05M sodium citrate, 30% (w/v) PEG 4,000, and 0.1M Tris‐HCl (pH 8.1). A total of 270 images were collected for the PHCP crystal at a camera length of 150 mm and an oscillation angle of 1.0°. The PHCP crystal diffracted to a maximal resolution of 1.89 Å (Table 2 ). The diffraction data sets were processed using CrystalClear (Rigaku, Japan). The PHCP crystal belonged to the space group P21221 (a = 54.24 Å, b = 72.92 Å, c = 132.37 Å), and had four PHCP molecules in an asymmetric unit, with a Matthews coefficient of 2.15 Å3/Da, which corresponds to a solvent content of 42.7%.34
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