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Open data
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Basic information
Entry | Database: PDB / ID: 3p4j | ||||||||||||||||||
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Title | Ultra-high resolution structure of d(CGCGCG)2 Z-DNA | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Z-DNA | Function / homology | SPERMINE / DNA | ![]() Method | ![]() ![]() ![]() ![]() Brzezinski, K. / Brzuszkiewicz, A. / Dauter, M. / Kubicki, M. / Jaskolski, M. / Dauter, Z. | ![]() ![]() Title: High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A. Authors: Brzezinski, K. / Brzuszkiewicz, A. / Dauter, M. / Kubicki, M. / Jaskolski, M. / Dauter, Z. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 28.2 KB | Display | ![]() |
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PDB format | ![]() | 19.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 364.2 KB | Display | ![]() |
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Full document | ![]() | 364.2 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 6.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ickS S: Starting model for refinement |
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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: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct #2: Chemical | ChemComp-SPM / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.7 Å3/Da / Density % sol: 27.77 % |
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Crystal grow | Temperature: 293 K / pH: 7 Details: DNA water solution mixed 1:1 v/v with 10% MPD, 12 mM spermine tetra-HCl, 40 mM HEPES pH 7.0 and equilibrated against 35% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2010 / Details: FOCUSING MIRRORS |
Radiation | Monochromator: SI 111 DOUBLE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.5904 Å / Relative weight: 1 |
Reflection | Resolution: 0.55→30 Å / Num. obs: 130650 / % possible obs: 84.5 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 2.45 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 0.55→0.57 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.276 / % possible all: 53 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ICK Resolution: 0.55→30 Å / Occupancy max: 1 / Occupancy min: 0.05 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: NONE Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE AND NON-RESTRAINED ANISOTROPIC REFINEMENT
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Refinement step | Cycle: LAST / Resolution: 0.55→30 Å
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