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Open data
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Basic information
Entry | Database: PDB / ID: 4qc7 | ||||||
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Title | Dodecamer structure of 5-formylcytosine containing DNA | ||||||
![]() | short DNA strands | ||||||
![]() | DNA / double helix / B-form DNA / 5-formylcytosine | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Szulik, M.W. / Pallan, P. / Egli, M. / Stone, M.P. | ||||||
![]() | ![]() Title: Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Authors: Szulik, M.W. / Pallan, P.S. / Nocek, B. / Voehler, M. / Banerjee, S. / Brooks, S. / Joachimiak, A. / Egli, M. / Eichman, B.F. / Stone, M.P. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.9 KB | Display | ![]() |
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PDB format | ![]() | 14.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 373.4 KB | Display | ![]() |
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Full document | ![]() | 373.5 KB | Display | |
Data in XML | ![]() | 3 KB | Display | |
Data in CIF | ![]() | 3.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4i9vC ![]() 4pwmC ![]() 436dS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3691.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized nucleic acid. #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 5% MPD, 20 mM Na Cacodylate, 6 mM Spermine tetra-HCl, 6 mM NaCl, 40 mM KCl , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 10, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 5842 / Num. obs: 5801 / % possible obs: 99.3 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 60 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 3.25 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 436D Resolution: 1.9→35.07 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.094 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(I): 5 / ESU R: 0.172 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→35.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.897→1.947 Å / Total num. of bins used: 20
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