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Yorodumi- PDB-6rvo: Multicrystal dataset of thaumatin collected using a multilayer mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rvo | ||||||
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Title | Multicrystal dataset of thaumatin collected using a multilayer monochromator. | ||||||
Components | Thaumatin I | ||||||
Keywords | PLANT PROTEIN / multilayer multicrystal VMXi | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Sandy, J. / Sanchez-Weatherby, J. / Mikolajek, H. / Winter, G. | ||||||
Citation | Journal: Iucrj / Year: 2023 Title: Protein-to-structure pipeline for ambient-temperature crystallography at VMXi Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.G. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rvo.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rvo.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 6rvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/6rvo ftp://data.pdbj.org/pub/pdb/validation_reports/rv/6rvo | HTTPS FTP |
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-Related structure data
Related structure data | 6rzpC 6selC 6svaC 1rqwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.3236085 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22228.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: Thaumatococcus daniellii (katemfe) / References: UniProt: P02883 |
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#2: Chemical | ChemComp-TLA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 16 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.9 % |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 5.6 / Details: 0.1 M Sodium citrate pH 5.6 0.75M Na/K Tartrate |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.979 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: May 22, 2019 / Details: Multilayer monochromator | |||||||||||||||||||||||||||
Radiation | Monochromator: Multilayer monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.97→58.56 Å / Num. obs: 19537 / % possible obs: 99.98 % / Redundancy: 38.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.409 / Rpim(I) all: 0.062 / Rrim(I) all: 0.414 / Net I/σ(I): 8.5 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RQW Resolution: 1.97→54.624 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→54.624 Å
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Refine LS restraints |
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LS refinement shell |
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