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Yorodumi- PDB-5c6i: Crystal Structure of Gadolinium derivative of HEWL solved using F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c6i | ||||||
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Title | Crystal Structure of Gadolinium derivative of HEWL solved using Free-Electron Laser radiation | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / lysozyme / XFEL / gadoteridol | ||||||
Function / homology | Function and homology information 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 | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Galli, L. / Barends, T.R.M. / Son, S.-K. / White, T.A. / Barty, A. / Botha, S. / Boutet, S. / Caleman, C. / Doak, R.B. / Nanao, M.H. ...Galli, L. / Barends, T.R.M. / Son, S.-K. / White, T.A. / Barty, A. / Botha, S. / Boutet, S. / Caleman, C. / Doak, R.B. / Nanao, M.H. / Nass, K. / Shoeman, R.L. / Timneanu, N. / Santra, R. / Schlichting, I. / Chapman, H.N. | ||||||
Citation | Journal: Iucrj / Year: 2015 Title: Towards phasing using high X-ray intensity. Authors: Galli, L. / Son, S.K. / Barends, T.R. / White, T.A. / Barty, A. / Botha, S. / Boutet, S. / Caleman, C. / Doak, R.B. / Nanao, M.H. / Nass, K. / Shoeman, R.L. / Timneanu, N. / Santra, R. / ...Authors: Galli, L. / Son, S.K. / Barends, T.R. / White, T.A. / Barty, A. / Botha, S. / Boutet, S. / Caleman, C. / Doak, R.B. / Nanao, M.H. / Nass, K. / Shoeman, R.L. / Timneanu, N. / Santra, R. / Schlichting, I. / Chapman, H.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c6i.cif.gz | 42.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c6i.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 5c6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c6i_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5c6i_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5c6i_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 5c6i_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/5c6i ftp://data.pdbj.org/pub/pdb/validation_reports/c6/5c6i | HTTPS FTP |
-Related structure data
Related structure data | 5c6jC 5c6lC 1h87S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 / Fragment: residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.94 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 3 Details: 20 % NaCl, 6 % PEG 6000, 1 M Na acetate pH 3.0, stored in 8% NaCl, 0.1 M sodium acetate buffer, pH 4.0, soaked in storage solution + 100 mM gadoteridol, batch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.463 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.463 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→56 Å / Num. obs: 10347 / % possible obs: 100 % / Redundancy: 20 % / Net I/σ(I): 18.17 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H87 Resolution: 1.9→35.44 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.14 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.149 / 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 max: 79.67 Å2 / Biso mean: 32.599 Å2 / Biso min: 18.09 Å2
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Refinement step | Cycle: final / Resolution: 1.9→35.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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