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- PDB-3dzr: Thaumatin by Classical hanging drop method before high X-Ray dose... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dzr | ||||||
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Title | Thaumatin by Classical hanging drop method before high X-Ray dose on ESRF ID29 beamline | ||||||
![]() | Thaumatin-1 | ||||||
![]() | PLANT PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tripathi, S. / Pechkova, E. / Nicolini, C. | ||||||
![]() | ![]() Title: Radiation damage in protein structural characterization by Synchrotron Radiation: State of the art and Nanotechnology-based perspective Authors: Pechkova, E. / Tripathi, S. / Nicolini, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.1 KB | Display | ![]() |
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PDB format | ![]() | 84.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3dnzC ![]() 3do0C ![]() 3do1C ![]() 3do2C ![]() 3dvqC ![]() 3dvrC ![]() 3dvsC ![]() 3dw1C ![]() 3dw3C ![]() 3dweC ![]() 3dznC ![]() 3dzpC ![]() 3e0aC ![]() 1rqwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22243.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-TLA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.4 % / Mosaicity: 0.33 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM ADA, 1M Na/K-tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2007 / Details: toroidal mirror |
Radiation | Monochromator: Si 311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→53.955 Å / Num. obs: 41007 / % possible obs: 100 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 |
Reflection shell | Resolution: 1.51→1.59 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 6.2 / Num. measured all: 45471 / Num. unique all: 5857 / Rsym value: 0.105 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RQW Resolution: 1.51→45.83 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.926 / SU B: 1.481 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.053 / 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 max: 148.79 Å2 / Biso mean: 16.559 Å2 / Biso min: 4.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→45.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.549 Å / Total num. of bins used: 20
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