+Open data
-Basic information
Entry | Database: PDB / ID: 1ejg | ||||||
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Title | CRAMBIN AT ULTRA-HIGH RESOLUTION: VALENCE ELECTRON DENSITY. | ||||||
Components | CRAMBIN (PRO22,SER22/LEU25,ILE25) | ||||||
Keywords | PLANT PROTEIN / VALENCE ELECTRON DENSITY / MULTI-SUBSTATE / MULTIPOLE REFINEMENT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Crambe hispanica subsp. abyssinica (Abyssinian crambe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.54 Å | ||||||
Authors | Jelsch, C. / Teeter, M.M. / Lamzin, V. / Pichon-Lesme, V. / Blessing, B. / Lecomte, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ejg.cif.gz | 34.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ejg.ent.gz | 27.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ejg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/1ejg ftp://data.pdbj.org/pub/pdb/validation_reports/ej/1ejg | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4738.447 Da / Num. of mol.: 1 / Fragment: CRAMBIN / Source method: isolated from a natural source Source: (natural) Crambe hispanica subsp. abyssinica (Abyssinian crambe) Species: Crambe hispanica / Strain: subsp. abyssinica / References: UniProt: P01542 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.4 Å3/Da / Density % sol: 30 % | ||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.54 |
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 |
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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.
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Refinement step | Cycle: LAST / Resolution: 0.54→22.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.54→0.57 Å
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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 |