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- PDB-5ebh: Crystal Structure HEW Lysozyme processed with the CrystalDirect a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ebh | ||||||
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Title | Crystal Structure HEW Lysozyme processed with the CrystalDirect automated mounting and cryo-cooling technology | ||||||
![]() | Lysozyme C | ||||||
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Function / homology | ![]() Lactose synthesis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquez, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Automated harvesting and processing of protein crystals through laser photoablation. Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Rower, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / ...Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Rower, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / Mathieu, M. / Cipriani, F. / Marquez, J.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 | ![]() | 71.5 KB | Display | ![]() |
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PDB format | ![]() | 52.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5amwC ![]() 5amxC ![]() 5amzC ![]() 5an4C ![]() 5andC ![]() 5aneC ![]() 5angC ![]() 5aniC ![]() 5anjC ![]() 5ankC ![]() 5anlC ![]() 5anoC ![]() 5dwpC ![]() 4b0dS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.06 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Crystallization experiments were carried out at the High Throughput Crystallization Laboratory of the EMBL Grenoble Outstation (https://embl.fr/htxlab) using the sitting-drop vapour ...Details: Crystallization experiments were carried out at the High Throughput Crystallization Laboratory of the EMBL Grenoble Outstation (https://embl.fr/htxlab) using the sitting-drop vapour diffusion method and CrystalDirect plates . Crystallization experiments were set up with 100 nl of sample and 100 nl of crystallization solution on the inner surface of the films within a CrystalDirect plate with a Cartesian PixSys robot (Cartesian Technologies). The crystallization solution was 0.1 M sodium acetate, pH=4.6 and 1.25 M sodium chloride. PH range: 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.2→19.7 Å / Num. obs: 37274 / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.2→1.22 Å |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4b0d Resolution: 1.2→19.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.494 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.046 / 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: 13.983 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→19.7 Å
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Refine LS restraints |
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