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- PDB-7jjv: Crystal waters on the nine polyproline type II helical bundle spr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jjv | ||||||
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Title | Crystal waters on the nine polyproline type II helical bundle springtail antifreeze protein from Granisotoma rainieri match the ice lattice | ||||||
![]() | GrAFP antifreeze protein | ||||||
![]() | ANTIFREEZE PROTEIN / glycine-rich / polyproline type II | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Scholl, C.L. / Tsuda, S. / Graham, L.A. / Davies, P.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal waters on the nine polyproline type II helical bundle springtail antifreeze protein from Granisotoma rainieri match the ice lattice. Authors: Scholl, C.L. / Tsuda, S. / Graham, L.A. / Davies, P.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87 KB | Display | ![]() |
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PDB format | ![]() | 64.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.4 KB | Display | ![]() |
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Full document | ![]() | 430.2 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pneS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10811.161 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.01 % |
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Crystal grow | Temperature: 277.15 K / Method: microbatch / Details: 0.2 M lithium nitrate, 2.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→43.171 Å / Num. obs: 52608 / % possible obs: 99.9 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Χ2: 0.9 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.21→1.23 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.925 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2579 / CC1/2: 0.923 / Rpim(I) all: 0.266 / Rrim(I) all: 0.963 / Χ2: 0.76 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PNE Resolution: 1.21→43.171 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.452 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04 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: 18.855 Å2
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Refinement step | Cycle: LAST / Resolution: 1.21→43.171 Å
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Refine LS restraints |
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LS refinement shell |
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