+Open data
-Basic information
Entry | Database: PDB / ID: 6w47 | ||||||
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Title | Peptoid-Containing Collagen Peptide | ||||||
Components | Collagen-like peptide | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Collagen / Triple Helix / CMP / Peptoid / STRUCTURAL PROTEIN | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å | ||||||
Authors | Chenoweth, D.M. / Melton, S.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chem Sci / Year: 2020 Title: Rules for the design of aza-glycine stabilized triple-helical collagen peptides. Authors: Melton, S.D. / Brackhahn, E.A.E. / Orlin, S.J. / Jin, P. / Chenoweth, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w47.cif.gz | 28.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w47.ent.gz | 20.3 KB | Display | PDB format |
PDBx/mmJSON format | 6w47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/6w47 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/6w47 | HTTPS FTP |
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-Related structure data
Related structure data | 6w46C 3abnS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein/peptide | Mass: 2423.597 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-EDO / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 1.57 Å3/Da / Density % sol: 21.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: Crystallization: 0.2 M Potassium formate, 20% PEG 3350 Cryoprotectant: 20% Glycercol Temp details: After |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→37.07 Å / Num. obs: 15857 / % possible obs: 95.75 % / Redundancy: 4.6 % / Biso Wilson estimate: 8.06 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.072 / Rrim(I) all: 0.122 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.15→1.191 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1215 / CC1/2: 0.823 / Rpim(I) all: 0.53 / Rrim(I) all: 0.796 / % possible all: 75.5 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ABN Resolution: 1.15→37.07 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.362 Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→37.07 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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