+Open data
-Basic information
Entry | Database: PDB / ID: 4zg3 | ||||||
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Title | In-vacuum long-wavelength crystallography | ||||||
Components | Thaumatin-1 | ||||||
Keywords | PLANT PROTEIN / thaumatin / in vacuum | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å | ||||||
Authors | Wagner, A. / Duman, R. / Henderson, K. / Mykhaylyk, V. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: In-vacuum long-wavelength macromolecular crystallography. Authors: Wagner, A. / Duman, R. / Henderson, K. / Mykhaylyk, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zg3.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zg3.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/4zg3 ftp://data.pdbj.org/pub/pdb/validation_reports/zg/4zg3 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883 | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.53 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 0.5 M K/Na Tartrate, 0.05 M ADA, ph6.8, 20 % glycerol |
-Data collection
Diffraction | Mean temperature: 45 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 1.378 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2014 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.378 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→150.37 Å / Num. obs: 138112 / % possible obs: 89.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.2 / % possible all: 79.9 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.2→53.986 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.26 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.17 Å2 / Biso mean: 15.8101 Å2 / Biso min: 8.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→53.986 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25
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