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- PDB-5a3z: Structure of monoclinic Lysozyme obtained by multi crystal data c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a3z | ||||||
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Title | Structure of monoclinic Lysozyme obtained by multi crystal data collection | ||||||
![]() | LYSOZYME | ||||||
![]() | HYDROLASE / MULTI CRYSTAL DATA COLLECTION / SYNCHROTRON SERIAL CRYSTALLOGRAPHY / SSX | ||||||
Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zander, U. / Bourenkov, G. / Popov, A.N. / de Sanctis, D. / McCarthy, A.A. / Svensson, O. / Round, E.S. / Gordeliy, V.I. / Mueller-Dieckmann, C. / Leonard, G.A. | ||||||
![]() | ![]() Title: Meshandcollect: An Automated Multi-Crystal Data-Collection Workflow for Synchrotron Macromolecular Crystallography Beamlines. Authors: Zander, U. / Bourenkov, G. / Popov, A.N. / De Sanctis, D. / Svensson, O. / Mccarthy, A.A. / Round, E. / Gordeliy, V. / Mueller-Dieckmann, C. / Leonard, G.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62 KB | Display | ![]() |
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PDB format | ![]() | 50 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.5 KB | Display | ![]() |
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Full document | ![]() | 459.2 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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Components
#1: Protein | Mass: 16257.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→19.73 Å / Num. obs: 23004 / % possible obs: 85 % / Observed criterion σ(I): 2.2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 |
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Processing
Software | Name: REFMAC / Version: 5.8.0103 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.59→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.069 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 17.302 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→20 Å
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Refine LS restraints |
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