+Open data
-Basic information
Entry | Database: PDB / ID: 6vuo | ||||||
---|---|---|---|---|---|---|---|
Title | Reverse Transcriptase Diabody with S82bC/R83T Mutation | ||||||
Components | Single-chain Fv | ||||||
Keywords | PROTEIN BINDING / Antibody fragment | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 Å | ||||||
Authors | Chelsy, C. / Arnold, E. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Structure / Year: 2021 Title: Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry. Authors: Chesterman, C. / Arnold, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6vuo.cif.gz | 279.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vuo.ent.gz | 229.7 KB | Display | PDB format |
PDBx/mmJSON format | 6vuo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vuo_validation.pdf.gz | 265.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6vuo_full_validation.pdf.gz | 265.2 KB | Display | |
Data in XML | 6vuo_validation.xml.gz | 1.5 KB | Display | |
Data in CIF | 6vuo_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/6vuo ftp://data.pdbj.org/pub/pdb/validation_reports/vu/6vuo | HTTPS FTP |
-Related structure data
Related structure data | 6vrpSC 6vugC 6vunC 6vupC 7kbmC 7kboC 7kbpC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 25444.207 Da / Num. of mol.: 2 / Mutation: S82bC, R83T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: scFv / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.13 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 14% PEG 1000, 0.1 M Sodium Citrate pH 5.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.449→50 Å / Num. obs: 124175 / % possible obs: 99.7 % / Redundancy: 12.2 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.057 / Net I/σ(I): 54.5 |
Reflection shell | Resolution: 1.45→1.5 Å / Rmerge(I) obs: 0.656 / Num. unique obs: 8188 / Rrim(I) all: 0.718 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VRP Resolution: 1.449→44.556 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.73 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.449→44.556 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|