+Open data
-Basic information
Entry | Database: PDB / ID: 4r49 | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Racemic crystal structure of a calcium-bound B-DNA duplex | ||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / racemic DNA / racemates | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | Authors | Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I. | Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 | Title: Racemic DNA crystallography. Authors: Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4r49.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4r49.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 4r49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r49_validation.pdf.gz | 378.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4r49_full_validation.pdf.gz | 378.8 KB | Display | |
Data in XML | 4r49_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 4r49_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/4r49 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/4r49 | HTTPS FTP |
-Related structure data
Related structure data | 4r44C 4r45C 4r47C 4r48C 4r4aC 4r4dC 3r86S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: DNA chain | Mass: 3045.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: B-DNA Duplex / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.51 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1 mM DNA, 50 mM sodium cacodylate, 2 M calcium chloride, 1 mM spermine, 40% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 14, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→34.25 Å / Num. all: 25176 / Num. obs: 23975 / % possible obs: 95.23 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 47.43 Å2 / Rmerge(I) obs: 0.0372 / Net I/σ(I): 9.69 |
Reflection shell | Resolution: 1.28→1.32 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.2656 / Mean I/σ(I) obs: 2.39 / % possible all: 91.68 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3R86 Resolution: 1.28→34.25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.437 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.318 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.28→34.25 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.28→1.313 Å / Total num. of bins used: 20
|