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- PDB-7q76: Room temperature structure of RNase A at 22 MPa helium gas pressu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7q76 | ||||||
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Title | Room temperature structure of RNase A at 22 MPa helium gas pressure in a sapphire capillary | ||||||
![]() | Ribonuclease pancreatic | ||||||
![]() | HYDROLASE / HPMX / high-pressure macromolecular crystallography / sapphire capillary | ||||||
Function / homology | ![]() pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lieske, J. / Guenther, S. / Saouane, S. / Meents, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Fixed-target high-pressure macromolecular crystallography Authors: Lieske, J. / Saouane, S. / Guenther, S. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, J. / Rarey, M. / Abdellatif, M.H. / ...Authors: Lieske, J. / Saouane, S. / Guenther, S. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, J. / Rarey, M. / Abdellatif, M.H. / Gabdulkhakov, A.G. / Selikhanov, G.K. / Chapman, H.N. / Meents, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.6 KB | Display | ![]() |
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PDB format | ![]() | 70 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.3 KB | Display | ![]() |
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Full document | ![]() | 433 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 10.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7q75C ![]() 7q77C ![]() 7q78C ![]() 7q79C ![]() 7q7aC ![]() 7q7bC ![]() 7q7dC ![]() 7q7eC ![]() 7q7fC ![]() 7q7gC ![]() 7q7hC ![]() 7q7jC ![]() 7q7mC ![]() 7q7nC ![]() 7q7oC ![]() 2e3wS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 10-20 mg/ml protein dissolved in 0.1 M sodium acetate pH 4.5 was mixed in a 1:1 ratio with precipitant containing 0.1 M sodium acetate pH 4.5, 1.2-1.5 M ammonium sulphate and 2-2.5 M sodium ...Details: 10-20 mg/ml protein dissolved in 0.1 M sodium acetate pH 4.5 was mixed in a 1:1 ratio with precipitant containing 0.1 M sodium acetate pH 4.5, 1.2-1.5 M ammonium sulphate and 2-2.5 M sodium chloride and equilibrated for one to two days at room-temperature. Pressure: 101.325 kPa |
-Data collection
Diffraction | Ambient environment: gaseous He / Ambient pressure: 22000 kPa / Mean temperature: 295 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: Sep 26, 2019 |
Diffraction measurement | Specimen support: sapphire capillary |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.477 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→25.65 Å / Num. obs: 26313 / % possible obs: 99.17 % / Redundancy: 8.4 % / Biso Wilson estimate: 21.28 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.0485 / Net I/σ(I): 7.44 |
Reflection shell | Resolution: 1.48→1.533 Å / Rmerge(I) obs: 2.128 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 2593 / CC1/2: 0.304 / CC star: 0.683 / Rpim(I) all: 0.7747 / % possible all: 98.67 |
Cell measurement | Pressure: 22000 kPa |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2E3W Resolution: 1.48→25.65 Å / SU ML: 0.1793 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.0956 / Stereochemistry target values: GeoStd + Monomer Library
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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: 33.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→25.65 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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