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Yorodumi- PDB-2w1m: THE INTERDEPENDENCE OF WAVELENGTH, REDUNDANCY AND DOSE IN SULFUR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w1m | ||||||
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Title | THE INTERDEPENDENCE OF WAVELENGTH, REDUNDANCY AND DOSE IN SULFUR SAD EXPERIMENTS: 2.070 A WAVELENGTH with 2theta 30 degrees data | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / RADIATION DAMAGE / REDUNDANCY / SAD / DOSE / WAVELENGTH / DETECTOR- TILT GEOMETRY | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å | ||||||
Authors | Cianci, M. / Helliwell, J.R. / Suzuki, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: The Interdependence of Wavelength, Redundancy and Dose in Sulfur Sad Experiments. Authors: Cianci, M. / Helliwell, J.R. / Suzuki, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w1m.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w1m.ent.gz | 35 KB | Display | PDB format |
PDBx/mmJSON format | 2w1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/2w1m ftp://data.pdbj.org/pub/pdb/validation_reports/w1/2w1m | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: P00698, lysozyme | ||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37 % Description: DATA COLLECTED WITH 2THETA ARM SET AT 30 DEGREES |
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Crystal grow | pH: 4.2 / Details: PLEASE SEE REFERENCE PAPER., pH 4.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 2.07 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 6, 2004 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→1.78 Å / Num. obs: 11476 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 25 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 49.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.78→55.3 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.574 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INTENSITIES (AND NOT STRUCTURE FACTORS) WERE SUBMITTED.
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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: 23.29 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→55.3 Å
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