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- PDB-3rz6: Neutron structure of perdeuterated rubredoxin using 40 hours 1st ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rz6 | ||||||
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Title | Neutron structure of perdeuterated rubredoxin using 40 hours 1st pass data | ||||||
![]() | Rubredoxin | ||||||
![]() | ELECTRON TRANSPORT / Iron / metal-binding / transport | ||||||
Function / homology | ![]() alkane catabolic process / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | NEUTRON DIFFRACTION / NUCLEAR REACTOR / ![]() | ||||||
![]() | Munshi, P. / Chung, C.-L. / Weiss, K.L. / Blakeley, M.P. / Myles, D.A.A. / Meilleur, F. | ||||||
![]() | ![]() Title: Rapid visualization of hydrogen positions in protein neutron crystallographic structures. Authors: Munshi, P. / Chung, S.L. / Blakeley, M.P. / Weiss, K.L. / Myles, D.A. / Meilleur, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 31 KB | Display | ![]() |
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PDB format | ![]() | 20.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 324.3 KB | Display | ![]() |
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Full document | ![]() | 324.2 KB | Display | |
Data in XML | ![]() | 2.3 KB | Display | |
Data in CIF | ![]() | 3.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rygC ![]() 3rztC ![]() 3ss2C ![]() 3kywS ![]() 3rzr 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
#1: Protein | Mass: 6031.728 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-DOD / |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 mg/ml rubredoxin in 1.9 M sodium/potassium phosphate sitting drop equilibrated against 3.8 m sodium/potassium phosphate reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 293 K | |||||||||
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Diffraction source | Source: NUCLEAR REACTOR / Site: ![]() ![]() | |||||||||
Detector | Type: MAATEL QLD: LADI-III / Detector: IMAGE PLATE / Date: May 7, 2008 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.65→27.243 Å / Num. all: 4783 / Num. obs: 4781 / % possible obs: 74.1 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.117 | |||||||||
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 2.9 / % possible all: 30.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3KYW Resolution: 1.75→21.766 Å / SU ML: 0.36 / σ(F): 1.56 / Phase error: 21.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.2 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.919 Å2 / ksol: 0.6 e/Å3 | ||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.75→21.766 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→21.7677 Å
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