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Yorodumi- PDB-9j1r: Structure of a triple-helix region of human Collagen type II from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9j1r | ||||||
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Title | Structure of a triple-helix region of human Collagen type II from Trautec | ||||||
Components | Triple-helix region of human collagen type II | ||||||
Keywords | STRUCTURAL PROTEIN / Human collagen II / Triple-helix | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Fan, X. / Chu, Y. / Zhai, Y. / Fu, S. / Li, D. / Cao, K. / Feng, P. / Wang, X. / Le, H. / Tang, D. ...Fan, X. / Chu, Y. / Zhai, Y. / Fu, S. / Li, D. / Cao, K. / Feng, P. / Wang, X. / Le, H. / Tang, D. / Zhang, F. / Qian, S. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of a triple-helix region of human Collagen type II from Trautec Authors: Fan, X. / Chu, Y. / Zhai, Y. / Fu, S. / Li, D. / Cao, K. / Feng, P. / Wang, X. / Le, H. / Tang, D. / Zhang, F. / Qian, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9j1r.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9j1r.ent.gz | 35 KB | Display | PDB format |
PDBx/mmJSON format | 9j1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/9j1r ftp://data.pdbj.org/pub/pdb/validation_reports/j1/9j1r | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2876.101 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.88 Å3/Da / Density % sol: 34.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Crystal-C7:0.2M (NH4)2SO4, 30% PEG4,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→46.62 Å / Num. obs: 11458 / % possible obs: 97.8 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.45→1.47 Å / Num. unique obs: 542 / CC1/2: 0.826 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1K6F Resolution: 1.45→46.62 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.317 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.084 Details: Hydrogens have been added in their riding positions
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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: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.276 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→46.62 Å
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Refine LS restraints |
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LS refinement shell |
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