+Open data
-Basic information
Entry | Database: PDB / ID: 1n6y | ||||||
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Title | RIP-phasing on Bovine Trypsin | ||||||
Components | Trypsinogen, cationic | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / digestion / serine protease inhibitor complex / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / RIP - Radiation-Damage Induced Phasing / Resolution: 1.4 Å | ||||||
Authors | Ravelli, R.B.G. / Leiros, H.-K.S. / Pan, B. / Caffrey, M. / McSweeney, S. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Specific Radiation-Damage Can Be Used To Solve Macromolecular Crystal Structures Authors: Ravelli, R.B.G. / Leiros, H.-K.S. / Pan, B. / Caffrey, M. / McSweeney, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n6y.cif.gz | 96.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n6y.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 1n6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/1n6y ftp://data.pdbj.org/pub/pdb/validation_reports/n6/1n6y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: pancreas / References: UniProt: P00760, trypsin |
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-Non-polymers , 5 types, 293 molecules
#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-ABN / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.67 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 25% polyethylene glycol (PEG) 8000, 0.2 M ammonium sulphate, 0.1 M Tris buffer, pH 8, and 100 mM benzylamine, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2001 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→42 Å / Num. all: 41043 / Num. obs: 40971 / % possible obs: 99.83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Biso Wilson estimate: 12.31 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.4→1.47 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 2.7 / % possible all: 97.4 |
Reflection | *PLUS Lowest resolution: 45 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 97.4 % |
-Processing
Software |
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Refinement | Method to determine structure: RIP - Radiation-Damage Induced Phasing Resolution: 1.4→42 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.695 / SU ML: 0.029 Isotropic thermal model: Anisotropic for protein and ligands. Water molecules are refined isotropic Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.054 Details: Model 1n6x was refined against data collected before the "X-ray burn" and used for some additional cycles of refinement against the data after the "X-ray burn". The resulting difference Fo- ...Details: Model 1n6x was refined against data collected before the "X-ray burn" and used for some additional cycles of refinement against the data after the "X-ray burn". The resulting difference Fo-Fc map shows features characteristic for radiation damage, such as negative density for the disulphides. This model has not been manually adjusted to these features! Structure was phased using X-ray damage alone
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.552 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 45 Å / Num. reflection obs: 40972 / Rfactor Rfree: 0.173 / Rfactor Rwork: 0.143 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 1.47 Å |