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- PDB-4j61: Crystal structure of Ribonuclease A soaked in 40% Cyclopentanone:... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j61 | ||||||
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Title | Crystal structure of Ribonuclease A soaked in 40% Cyclopentanone: One of twelve in MSCS set | ||||||
![]() | Ribonuclease pancreatic | ||||||
![]() | HYDROLASE / Endoribonuclease | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Kearney, B.M. / Dechene, M. / Swartz, P.D. / Mattos, C. | ||||||
![]() | ![]() Title: DRoP: A program for analysis of water structure on protein surfaces Authors: Kearney, B.M. / Roberts, D. / Dechene, M. / Swartz, P.D. / Mattos, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.8 KB | Display | ![]() |
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PDB format | ![]() | 27.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4j5zC ![]() 4j60C ![]() 4j62C ![]() 4j63C ![]() 4j64C ![]() 4j65C ![]() 4j66C ![]() 4j67C ![]() 4j68C ![]() 4j69C ![]() 4j6aC ![]() 1rphS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pancreas / Source: (natural) ![]() ![]() | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-MFW / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 35% ammonium sulfate, 1.5 M sodium chloride, 35 mg/mL protein in 20 mM sodium phosphate buffer, pH 6.0, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2004 / Details: mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.69→50 Å / Num. all: 17106 / Num. obs: 17106 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.8 % / Rmerge(I) obs: 0.076 / Χ2: 1.349 / Net I/σ(I): 9.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RPH Resolution: 1.69→41.675 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.13 / σ(F): 1.35 / Phase error: 18.16 / Stereochemistry target values: ML
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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 max: 60.24 Å2 / Biso mean: 23.3661 Å2 / Biso min: 10.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→41.675 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %
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