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- PDB-4e3u: Crystal Structure of Hen Egg White Lysozyme Cryoprotected in Proline -
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Open data
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Basic information
Entry | Database: PDB / ID: 4e3u | ||||||
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Title | Crystal Structure of Hen Egg White Lysozyme Cryoprotected in Proline | ||||||
![]() | Lysozyme C | ||||||
![]() | ![]() | ||||||
Function / homology | ![]() Lactose synthesis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tanner, J.J. / Pemberton, T.A. | ||||||
![]() | ![]() Title: Proline: Mother Nature's cryoprotectant applied to protein crystallography. Authors: Pemberton, T.A. / Still, B.R. / Christensen, E.M. / Singh, H. / Srivastava, D. / Tanner, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.9 KB | Display | ![]() |
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PDB format | ![]() | 45.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4e3vC ![]() 4e3wC ![]() 4e3xC ![]() 2lyzS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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 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 / Details: Egg White / Source: (natural) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-PRO / ![]() | ||
#3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.58 % |
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Crystal grow![]() | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1.0M sodium chloride, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 123 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 25, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→19.499 Å / Num. all: 19076 / Num. obs: 19076 / % possible obs: 99.6 % / Redundancy: 10.8 % / Rsym value: 0.028 / Net I/σ(I): 46.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 2LYZ Resolution: 1.5→19.499 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8454 / SU ML: 0.21 / σ(F): 0 / Phase error: 21.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.412 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.34 Å2 / Biso mean: 17.3662 Å2 / Biso min: 8.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.499 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: -0.994 Å / Origin y: 19.9158 Å / Origin z: 19.313 Å
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Refinement TLS group | Selection details: Chain A |