+Open data
-Basic information
Entry | Database: PDB / ID: 5mhe | |||||||||
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Title | Crystal structure of anti-T4 Fab fragment with T4 | |||||||||
Components | (Fab-fragment) x 2 | |||||||||
Keywords | IMMUNE SYSTEM / Fab-fragment / Ig fold | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 3,5,3',5'-TETRAIODO-L-THYRONINE Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Parkkinen, T. / Rouvinen, J. | |||||||||
Citation | Journal: To Be Published Title: Crystal structures of anti-T4 Fab fragment Authors: Parkkinen, T. / Rouvinen, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mhe.cif.gz | 175.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mhe.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mhe_validation.pdf.gz | 835.5 KB | Display | wwPDB validaton report |
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Full document | 5mhe_full_validation.pdf.gz | 839.7 KB | Display | |
Data in XML | 5mhe_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 5mhe_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/5mhe ftp://data.pdbj.org/pub/pdb/validation_reports/mh/5mhe | HTTPS FTP |
-Related structure data
Related structure data | 5mhgC 1dqdS 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 on special symmetry positions |
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-Components
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 23323.686 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): RV308 |
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#2: Antibody | Mass: 25367.357 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): RV308 |
-Non-polymers , 4 types, 339 molecules
#3: Chemical | ChemComp-SO4 / | ||
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#4: Chemical | ChemComp-T44 / | ||
#5: Chemical | #6: 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: 2.27 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1 M ammonium sulphate, 25% PEG 3350, 0.1 M Hepes |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 63198 / % possible obs: 93.6 % / Redundancy: 1.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.119 / Net I/σ(I): 7.66 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 0.65 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 1.49 / CC1/2: 0.6 / Rrim(I) all: 1.05 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DQD Resolution: 1.9→19.835 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.835 Å
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Refine LS restraints |
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LS refinement shell |
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