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Open data
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Basic information
Entry | Database: PDB / ID: 2raz | ||||||
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Title | 4-(methylthio)nitrobenzene in complex with T4 lysozyme L99A | ||||||
![]() | Lysozyme![]() | ||||||
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Function / homology | ![]() viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Graves, A.P. / Boyce, S.E. / Shoichet, B.K. | ||||||
![]() | ![]() Title: Rescoring docking hit lists for model cavity sites: predictions and experimental testing. Authors: Graves, A.P. / Shivakumar, D.M. / Boyce, S.E. / Jacobson, M.P. / Case, D.A. / Shoichet, B.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54 KB | Display | ![]() |
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PDB format | ![]() | 37.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2rayC ![]() 2rb0C ![]() 2rb1C ![]() 2rb2C ![]() 2rbnC ![]() 2rboC ![]() 2rbpC ![]() 2rbqC ![]() 2rbrC ![]() 2rbsC ![]() 2rbtC ![]() 2rbuC ![]() 2rbvC ![]() 2rbwC ![]() 2rbxC ![]() 2rbyC ![]() 2rbzC ![]() 2rc0C ![]() 2rc1C ![]() 2rc2C ![]() 184lS C: citing same article ( 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: 18359.023 Da / Num. of mol.: 1 / Mutation: L99A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ![]() #3: Chemical | ChemComp-259 / | #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.59 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 8, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.64→52.27 Å / Num. all: 25643 / Num. obs: 25592 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.061 / Χ2: 1.004 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.454 / Num. unique all: 2520 / Χ2: 1.004 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 184L Resolution: 1.641→52.27 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.632 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.366 Å2
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Refinement step | Cycle: LAST / Resolution: 1.641→52.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.641→1.683 Å / Total num. of bins used: 20
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