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- PDB-7lqc: X-ray radiation damage series on Proteinase K at 277K, multi-conf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lqc | ||||||
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Title | X-ray radiation damage series on Proteinase K at 277K, multi-conformer model, dataset 4 (merged) | ||||||
![]() | Proteinase K![]() | ||||||
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Function / homology | ![]() peptidase K / serine-type endopeptidase activity / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yabukarski, F. / Doukov, T. / Herschlag, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals. Authors: Yabukarski, F. / Doukov, T. / Mokhtari, D.A. / Du, S. / Herschlag, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 345.7 KB | Display | ![]() |
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PDB format | ![]() | 243.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7lfgC ![]() 7ljvC ![]() 7ljwC ![]() 7ljzC ![]() 7lk5C ![]() 7lk6C ![]() 7llpC ![]() 7ln7SC ![]() 7ln8C ![]() 7ln9C ![]() 7lnbC ![]() 7lncC ![]() 7lndC ![]() 7loqC ![]() 7lorC ![]() 7lp6C ![]() 7lplC ![]() 7lpmC ![]() 7lptC ![]() 7lpuC ![]() 7lpvC ![]() 7lq8C ![]() 7lq9C ![]() 7lqaC ![]() 7lqbC ![]() 7ltdC ![]() 7ltiC ![]() 7ltvC ![]() 7lu0C ![]() 7lu1C ![]() 7lu2C ![]() 7lu3C 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
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#2: Chemical | ![]() #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.22 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Proteinase K was dissolved in 10 mM Calcium Chloride, 50 mM Tris pH 7.5 at a final concentration of 30 mg/ml. 1-2 microliters of this protein solution was mixed with an equivalent volume of ...Details: Proteinase K was dissolved in 10 mM Calcium Chloride, 50 mM Tris pH 7.5 at a final concentration of 30 mg/ml. 1-2 microliters of this protein solution was mixed with an equivalent volume of precipitant solution (1.0 M Ammonium Sulfate). |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.02→34.89 Å / Num. obs: 120685 / % possible obs: 100 % / Redundancy: 67.6 % / Biso Wilson estimate: 10.68 Å2 / Rmerge(I) obs: 0.625 / Rpim(I) all: 0.082 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.02→1.04 Å / Redundancy: 46.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5861 / Rpim(I) all: 8.158 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7LN7 Resolution: 1.02→33.92 Å / SU ML: 0.0993 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.558 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.02→33.92 Å
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Refine LS restraints |
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LS refinement shell |
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