+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ejg | ||||||
---|---|---|---|---|---|---|---|
Title | CRAMBIN AT ULTRA-HIGH RESOLUTION: VALENCE ELECTRON DENSITY. | ||||||
![]() | CRAMBIN (PRO22,SER22/LEU25,ILE25) | ||||||
![]() | PLANT PROTEIN / VALENCE ELECTRON DENSITY / MULTI-SUBSTATE / MULTIPOLE REFINEMENT | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jelsch, C. / Teeter, M.M. / Lamzin, V. / Pichon-Lesme, V. / Blessing, B. / Lecomte, C. | ||||||
![]() | ![]() Title: Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin. Authors: Jelsch, C. / Teeter, M.M. / Lamzin, V. / Pichon-Pesme, V. / Blessing, R.H. / Lecomte, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 34.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 27.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 370.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 370.8 KB | Display | |
Data in XML | ![]() | 3 KB | Display | |
Data in CIF | ![]() | 3.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 4738.447 Da / Num. of mol.: 1 / Fragment: CRAMBIN / Source method: isolated from a natural source Source: (natural) ![]() Species: Crambe hispanica / Strain: subsp. abyssinica / References: UniProt: P01542 |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.4 Å3/Da / Density % sol: 30 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: The protein (40 mg/ml in 80% ethanol) is equilibrated against 60% ethanol. Not buffered., pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: Teeter, M.M., (1993) J. Mol. Biol., 230, 292. | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 31, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.54 Å / Relative weight: 1 |
Reflection | Resolution: 0.54→50 Å / Num. obs: 79868 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Biso Wilson estimate: 2.8 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 0.54→0.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.1476 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 0.54 Å / Lowest resolution: 50 Å / Num. all: 112293 / Num. obs: 79869 / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Num. measured all: 489969 |
Reflection shell | *PLUS Redundancy: 3.8 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 0.54→22.37 Å / σ(F): 0 Details: SHELX97 FOLLOWED BY MOLLY (N.K.HANSEN & P.COPPENS ACTA CRYSTALLOGR. A34, 909-921) REFINEMENT OF ELECTRON DENSITY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.54→22.37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 0.54→0.57 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: SHELXL97 DICTIONARY | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: MOLLY / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.09 / Rfactor Rwork: 0.09 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 2.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.205 / % reflection Rfree: 5 % / Rfactor Rwork: 0.197 |