+Open data
-Basic information
Entry | Database: PDB / ID: 1il1 | ||||||
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Title | Crystal structure of G3-519, an anti-HIV monoclonal antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / beta sheet structure / antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Berry, M.B. / Johnson, K.A. / Radding, W. / Fung, M. / Liou, R. / Phillips Jr., G.N. | ||||||
Citation | Journal: Proteins / Year: 2001 Title: Structure of an anti-HIV monoclonal Fab antibody fragment specific to a gp120 C-4 region peptide. Authors: Berry, M.B. / Johnson, K.A. / Radding, W. / Fung, M. / Liou, R. / Phillips Jr., G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1il1.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1il1.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 1il1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1il1_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
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Full document | 1il1_full_validation.pdf.gz | 441.7 KB | Display | |
Data in XML | 1il1_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 1il1_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/1il1 ftp://data.pdbj.org/pub/pdb/validation_reports/il/1il1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23559.076 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) Cell line: mouse myeloma line SP2/0 fused with antibody expressing B cells |
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#2: Antibody | Mass: 24514.133 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) Cell line: mouse myeloma line SP2/0 fused with antibody expressing B cells |
#3: 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: 2.18 Å3/Da / Density % sol: 43.69 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2M ammonium sulfate, 200mM sodium chloride, 100mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||
Crystal grow | *PLUS Details: used microseeding / PH range low: 6 / PH range high: 5 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 22, 1997 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.74 Å / Num. all: 18605 / Num. obs: 18605 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.505 / % possible all: 88.1 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.74 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 124012.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.51 Å2 / ksol: 0.345 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.33 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor Rfree: 0.247 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.351 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.288 |