+Open data
-Basic information
Entry | Database: PDB / ID: 6w46 | ||||||
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Title | Valine-Containing Collagen Peptide | ||||||
Components | Collagen-like peptide | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Collagen / Triple Helix / CMP / Structural Protein | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 | 6w46.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w46.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 6w46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w46_validation.pdf.gz | 446.9 KB | Display | wwPDB validaton report |
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Full document | 6w46_full_validation.pdf.gz | 450.3 KB | Display | |
Data in XML | 6w46_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 6w46_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/6w46 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/6w46 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein/peptide | Mass: 2847.886 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: 1.75 Å3/Da / Density % sol: 29.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: Crystallization: 0.01 M Li2SO4 Monohydrate, 0.094 M Tris HCl, 30% PEG 4000 Cryoprotectant: 20% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9198 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9198 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→37.24 Å / Num. obs: 16476 / % possible obs: 97.47 % / Redundancy: 2.9 % / Biso Wilson estimate: 8.83 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.08 / Rrim(I) all: 0.141 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.25→1.295 Å / Redundancy: 3 % / Rmerge(I) obs: 1.081 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1611 / CC1/2: 0.574 / Rpim(I) all: 0.736 / Rrim(I) all: 1.314 / % possible all: 96.44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→37.24 Å / SU ML: 0.166 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.243
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→37.24 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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