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Open data
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Basic information
Entry | Database: PDB / ID: 7z7l | |||||||||
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Title | REP-related Chom18 variant with double AC mismatch | |||||||||
![]() | Chom18-AC DNA | |||||||||
![]() | DNA / Mismatch / Non-canonical / Base pair / Double helix | |||||||||
Function / homology | STRONTIUM ION / DNA / DNA (> 10)![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Svoboda, J. / Schneider, B. / Berdar, D. / Kolenko, P. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.7 KB | Display | ![]() |
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PDB format | ![]() | 11.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 367.5 KB | Display | ![]() |
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Full document | ![]() | 367.9 KB | Display | |
Data in XML | ![]() | 2.4 KB | Display | |
Data in CIF | ![]() | 2.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z7kC ![]() 7z7mC ![]() 7z7uC ![]() 7z7wC ![]() 7z7yC ![]() 7z7zC ![]() 7z81C ![]() 7z82C ![]() 6rosS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 5503.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: Chemical | ChemComp-SR / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.37 % |
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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 |
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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: 2.5→37.76 Å / Num. obs: 2423 / % possible obs: 99.9 % / Redundancy: 23.4 % / Biso Wilson estimate: 82.44 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.011 / Rrim(I) all: 0.052 / Χ2: 1 / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 2.5→2.61 Å / Redundancy: 26 % / Rmerge(I) obs: 1.505 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 268 / CC1/2: 0.91 / Rpim(I) all: 0.295 / Rrim(I) all: 1.534 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ROS Resolution: 2.5→22.68 Å / SU ML: 0.3551 / Cross valid method: FREE R-VALUE / Phase error: 31.4069 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.65 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→22.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å
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