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Yorodumi- PDB-2oqn: High Pressure Cryocooling of Capillary Sample Cryoprotection and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oqn | ||||||
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Title | High Pressure Cryocooling of Capillary Sample Cryoprotection and Diffraction Phasing at Long Wavelengths | ||||||
Components | Thaumatin-1 | ||||||
Keywords | PLANT PROTEIN / high pressure cryocooling / capillary cryoprotection / sulfur SAD phasing | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kim, C.U. / Hao, Q. / Gruner, S.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: High-pressure cryocooling for capillary sample cryoprotection and diffraction phasing at long wavelengths. Authors: Kim, C.U. / Hao, Q. / Gruner, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oqn.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oqn.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 2oqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/2oqn ftp://data.pdbj.org/pub/pdb/validation_reports/oq/2oqn | HTTPS FTP |
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-Related structure data
Related structure data | 2oquC 1lxzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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 | ChemComp-TAR / |
#3: 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: 2.85 Å3/Da / Density % sol: 56.79 % |
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Crystal grow | Temperature: 293 K Method: crystallized in a polycarbonate capillary by vapor diffusion pH: 7 Details: 0.9 M sodium potassium tartrate, pH 7.0, Crystallized in a polycarbonate capillary by vapor diffusion , temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.7463 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2006 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7463 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 20909 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 17.1 Å2 / Rsym value: 0.089 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 5 / Rsym value: 0.175 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1lxz Resolution: 1.9→28.99 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.605 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.117 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→28.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.904→1.954 Å / Total num. of bins used: 20
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