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- PDB-8dz7: Hen lysozyme in orthorhombic space group at ambient temperature -... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dz7 | ||||||||||||||||||
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Title | Hen lysozyme in orthorhombic space group at ambient temperature - diffuse scattering dataset | ||||||||||||||||||
![]() | Lysozyme C | ||||||||||||||||||
![]() | HYDROLASE / ROOM TEMPERATURE / DIFFUSE SCATTERING / LYSOZYME | ||||||||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Meisburger, S.P. / Imran, S.M.S. / Ando, N. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Robust total X-ray scattering workflow to study correlated motion of proteins in crystals. Authors: Meisburger, S.P. / Case, D.A. / Ando, N. #1: ![]() Title: Robust total X-ray scattering workflow to study correlated motion of proteins in crystals Authors: Meisburger, S.P. / Case, D.A. / Ando, N. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109 KB | Display | ![]() |
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PDB format | ![]() | 80.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8dyzC ![]() 1wtmS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % |
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Crystal grow | Temperature: 318 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Reservoir contained 1.0-1.1 M NaCl, 0.1 M NaOAc pH 4.6. Drops of 30 microliters contained a 1:2 ratio of 90-100 mg/mL protein and reservoir solution. Temp details: The trays were set up at room temperature, incubated at 45 degC until crystals appeared, then returned to room temperature |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2016 / Details: 100 micron collimator | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.34→44.82 Å / Num. obs: 28707 / % possible obs: 96.9 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.011 / Rrim(I) all: 0.041 / Χ2: 1.02 / Net I/σ(I): 36 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1wtm Resolution: 1.34→44.82 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.029 / SU ML: 0.019 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.037 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.948 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→44.82 Å
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Refine LS restraints |
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LS refinement shell |
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