+Open data
-Basic information
Entry | Database: PDB / ID: 3mck | ||||||
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Title | Crystal structure of anti-beta-amyloid antibody C705 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / MONOCLONAL ANTIBODY | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Teplyakov, A. / Obmolova, G. / Gilliland, G.L. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Antibody modeling assessment. Authors: Almagro, J.C. / Beavers, M.P. / Hernandez-Guzman, F. / Maier, J. / Shaulsky, J. / Butenhof, K. / Labute, P. / Thorsteinson, N. / Kelly, K. / Teplyakov, A. / Luo, J. / Sweet, R. / Gilliland, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mck.cif.gz | 184.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mck.ent.gz | 146.6 KB | Display | PDB format |
PDBx/mmJSON format | 3mck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/3mck ftp://data.pdbj.org/pub/pdb/validation_reports/mc/3mck | HTTPS FTP |
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-Related structure data
Related structure data | 1e4xS S: Starting model for refinement |
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Similar 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
#1: Antibody | Mass: 24117.834 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Cell (production host): Human embryonic kidney (HEK) 293 cells Production host: HOMO SAPIENS (human) #2: Antibody | Mass: 24314.346 Da / Num. of mol.: 2 / Fragment: FD fragment of the heavy chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Cell (production host): Human embryonic kidney (HEK) 293 cells Production host: HOMO SAPIENS (human) #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 25% PEG 8K, 0.2 M LITHIUM SULFATE, 0.1 M SODIUM ACETATE PH 4.5; CRYO CONDITIONS: MOTHER LIQUOR + 15% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 19, 2006 / Details: VARIMAX HF |
Radiation | Monochromator: NONE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 42606 / Num. obs: 42606 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.429 / % possible all: 79.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E4X Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.765 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.226 / Stereochemistry target values: Engh & Huber
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.347 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.358 Å / Total num. of bins used: 20
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