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Open data
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Basic information
Entry | Database: PDB / ID: 1rf0 | ||||||
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Title | Crystal Structure of Fragment D of gammaE132A Fibrinogen | ||||||
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Function / homology | ![]() platelet maturation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kostelansky, M.S. / Gorkun, O.V. / Lord, S.T. | ||||||
![]() | ![]() Title: Calcium-Binding Site beta2, Adjacent to the "b" Polymerization Site, Modulates Lateral Aggregation of Protofibrils during Fibrin Polymerization. Authors: Kostelansky, M.S. / Lounes, K.C. / Ping, L.F. / Dickerson, S.K. / Gorkun, O.V. / Lord, S.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 275.5 KB | Display | ![]() |
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PDB format | ![]() | 221.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1rf1C ![]() 1lt9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 7747.030 Da / Num. of mol.: 2 / Fragment: Fibrinogen alpha/alpha-E Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | ![]() Mass: 35940.215 Da / Num. of mol.: 2 / Fragment: Fibrinogen Bbeta Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Protein | ![]() Mass: 35159.957 Da / Num. of mol.: 2 / Fragment: Fibrinogen gamma chain / Mutation: E132A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Sugars , 1 types, 2 molecules ![](data/chem/img/NAG.gif)
#4: Sugar | ![]() |
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-Non-polymers , 2 types, 122 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.38 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 14-15% PEG 3350, 70 mM calcium chloride, 2 mM sodium azide, 50 mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 11, 2003 Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) |
Radiation | Monochromator: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→18 Å / Num. all: 46581 / Num. obs: 46581 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 66 Å2 / Rsym value: 0.11 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 3.4 / Num. unique all: 4570 / Rsym value: 0.408 / % possible all: 99.6 |
Reflection | *PLUS Lowest resolution: 18 Å / Num. measured all: 186713 / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 99.6 % / Rmerge(I) obs: 0.408 |
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Processing
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Refinement | Method to determine structure![]() Starting model: 1LT9 Resolution: 2.81→17.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1750722.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.0889 Å2 / ksol: 0.318139 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.81→17.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 18 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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