+Open data
-Basic information
Entry | Database: PDB / ID: 6xym | ||||||
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Title | Nbe-LBM | ||||||
Components | Nbe-LBM | ||||||
Keywords | IMMUNE SYSTEM / Nanobody | ||||||
Function / homology | TERBIUM(III) ION Function and homology information | ||||||
Biological species | Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å | ||||||
Authors | Pompidor, G. / Zimmermann, S. / Loew, C. / Schneider, T. | ||||||
Citation | Journal: To Be Published Title: Engineered nanobodies with a lanthanide binding motif for crystallographic phasing Authors: Pompidor, G. / Zimmermann, S. / Loew, C. / Schneider, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xym.cif.gz | 129.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xym.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 6xym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/6xym ftp://data.pdbj.org/pub/pdb/validation_reports/xy/6xym | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15582.064 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30 %(w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→63.85 Å / Num. obs: 81806 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.025 / Rrim(I) all: 0.09 / Net I/σ(I): 15.9 / Num. measured all: 1061978 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.2→60.73 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1949 / WRfactor Rwork: 0.1458 / FOM work R set: 0.7203 / SU B: 2.492 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0385 / SU Rfree: 0.0422 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.042 / 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: 178.26 Å2 / Biso mean: 32.637 Å2 / Biso min: 11.85 Å2
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Refinement step | Cycle: final / Resolution: 1.2→60.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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