+
Open data
-
Basic information
Entry | Database: PDB / ID: 7z7u | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | REP-related Chom18 variant with double CG base pair | |||||||||
![]() | Chom18-CG DNA | |||||||||
![]() | DNA / Mismatch / Non-canonical / Base pair / Double helix | |||||||||
Function / homology | STRONTIUM ION / DNA / DNA (> 10)![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Svoboda, J. / Kolenko, P. / Berdar, D. / Schneider, B. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Conformation-based refinement of 18-mer DNA structures. Authors: Svoboda, J. / Berdar, D. / Kolenko, P. / Cerny, J. / Novakova, Z. / Pavlicek, J. / Schneider, B. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 24.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 11.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 355 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 355.5 KB | Display | |
Data in XML | ![]() | 1.9 KB | Display | |
Data in CIF | ![]() | 2.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z7kC ![]() 7z7lC ![]() 7z7mC ![]() 7z7wC ![]() 7z7yC ![]() 7z7zC ![]() 7z81C ![]() 7z82C ![]() 6rosS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 5519.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
---|---|
#2: Chemical | ChemComp-SR / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.55 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Natrix crystallization screen (Hampton Research) precipitant 18-22% (+/-)-2-Methyl-2,4-pentanediol buffer 0.04 M Sodium cacodylate trihydrate salt 0.04 M Magnezium chloride hexahydrate 0.08 ...Details: Natrix crystallization screen (Hampton Research) precipitant 18-22% (+/-)-2-Methyl-2,4-pentanediol buffer 0.04 M Sodium cacodylate trihydrate salt 0.04 M Magnezium chloride hexahydrate 0.08 M Strontium chloride hexahydrate additive 0.012 M spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2021 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→43.66 Å / Num. obs: 1958 / % possible obs: 100 % / Redundancy: 22.8 % / Biso Wilson estimate: 101.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.013 / Rrim(I) all: 0.061 / Χ2: 1.02 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 2.75→2.92 Å / Redundancy: 25 % / Rmerge(I) obs: 1.982 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 297 / CC1/2: 0.895 / Rpim(I) all: 0.4 / Rrim(I) all: 2.023 / Χ2: 1.04 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6ROS Resolution: 2.75→23 Å / SU ML: 0.4313 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3689 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 105 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→23 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.85 Å
|