+
Open data
-
Basic information
Entry | Database: PDB / ID: 1jy5 | ||||||
---|---|---|---|---|---|---|---|
Title | RNase-related protein from Calystegia sepium | ||||||
![]() | CalsepRRP | ||||||
![]() | HYDROLASE / RNase / alpha-beta protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rabijns, A. / Verboven, C. / Rouge, P. / Barre, A. / Van Damme, E.J.M. / Peumans, W.J. / De Ranter, C.J. | ||||||
![]() | ![]() Title: Structure of an RNase-related protein from Calystegia sepium. Authors: Rabijns, A. / Verboven, C. / Rouge, P. / Barre, A. / Van Damme, E.J. / Peumans, W.J. / De Ranter, C.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 98.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 75 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 447.7 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dixS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 23399.148 Da / Num. of mol.: 2 / Fragment: residues 1-212 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.21 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: NaCl, 0.1M acetate buffer, MPD, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 16, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9116 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. all: 163993 / Num. obs: 140214 / % possible obs: 85.5 % / Observed criterion σ(F): 1.41 / Observed criterion σ(I): 2 / Redundancy: 4.63 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 20.71 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 4.03 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 5.12 / Num. unique all: 1739 / Rsym value: 0.338 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 35416 / Num. measured all: 163993 |
Reflection shell | *PLUS % possible obs: 66.3 % / Num. unique obs: 1739 / Num. measured obs: 7023 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DIX Resolution: 2.05→27.63 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→27.63 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.012
| |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.2074 / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.2074 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.222 |