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Yorodumi- PDB-2by5: Is radiation damage dependent on the dose-rate used during macrom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2by5 | |||||||||
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Title | Is radiation damage dependent on the dose-rate used during macromolecular crystallography data collection | |||||||||
Components | CATIONIC TRYPSIN | |||||||||
Keywords | HYDROLASE / DATA COLLECTION / RADIATION DAMAGE / DOSE-RATE / SYNCHROTRON RADIATION | |||||||||
Function / homology | Function and homology information cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | |||||||||
Biological species | BOS TAURUS (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.3 Å | |||||||||
Authors | Leiros, H.-K.S. / Timmins, J. / Ravelli, R.B.G. / McSweeney, S.M. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Is Radiation Damage Dependent on the Dose-Rate Used During Macromolecular Crystallography Data Collection? Authors: Leiros, H.-K.S. / Timmins, J. / Ravelli, R.B.G. / Mcsweeney, S.M. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2by5.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2by5.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 2by5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2by5_validation.pdf.gz | 337.9 KB | Display | wwPDB validaton report |
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Full document | 2by5_full_validation.pdf.gz | 339.7 KB | Display | |
Data in XML | 2by5_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 2by5_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/2by5 ftp://data.pdbj.org/pub/pdb/validation_reports/by/2by5 | HTTPS FTP |
-Related structure data
Related structure data | 2bxyC 2bxzC 2by0C 2by1C 2by2C 2by3C 2by6C 2by7C 2by8C 2by9C 2byaC 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
-Protein , 1 types, 1 molecules X
#1: Protein | Mass: 25444.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P00760, trypsin |
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-Non-polymers , 5 types, 427 molecules
#2: Chemical | ChemComp-BEN / | ||||
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#3: Chemical | ChemComp-GOL / | ||||
#4: Chemical | #5: Chemical | ChemComp-CA / | #6: 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: 1.73 Å3/Da / Density % sol: 28.3 % |
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Crystal grow | Details: 25% PEG 8000, 0.2 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→20 Å / Num. obs: 52088 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 7.67 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.3→19.8 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.057 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.038 / 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: 7.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→19.8 Å
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Refine LS restraints |
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