 Entry |
| Summary |
| Database / ID | EM DATA BANK (EMDB) / 1612 |
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| Title | Nanoscale DNA box
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| Map | 3D Map of DNA Box |
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| Sample | DNA Box |
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| Keywords |  DNA box, origami, self-assembly, lid, nanoscale |
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| Authors | Andersen ES, Dong M, Nielsen MM, Jahn K, Subramani R, Mamdouh W, Golas MM, Sander B, Stark H, Oliveira CL, Pedersen JS, Birkedal V, Besenbacher F, Gothelf KV, Kjems J |
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| Date | Deposition: 2009-03-28, Header release: 2009-04-15, Map release: 2011-04-26, Last update: 2012-10-24 |
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| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
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| Structure Visualization |
| Movies |  Movie Page
#1: Surface view with section colored by density value, Surface level: 0.065, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.065, Made by UCSF CHIMERA |
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| Supplemental images |
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| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
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| Related Structure Data |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
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 Article |
| Citation - Primary |
| Article | Nature, Vol. 459, Issue 7243, Page 73-6, Year 2009 |
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| Title | Self-assembly of a nanoscale DNA box with a controllable lid. |
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| Authors | Ebbe S Andersen, Mingdong Dong, Morten M Nielsen, Kasper Jahn, Ramesh Subramani, Wael Mamdouh, Monika M Golas, Bjoern Sander, Holger Stark, Cristiano L P Oliveira, Jan Skov Pedersen, Victoria Birkedal, Flemming Besenbacher, Kurt V Gothelf, Jørgen Kjems
Danish National Research Foundation: Centre for DNA Nanotechnology. |
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| Keywords | Cryoelectron Microscopy, DNA (chemistry, 9007-49-2), Imaging, Three-Dimensional, Microscopy, Atomic Force, Nanostructures (chemistry), Nucleic Acid Conformation |
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| Links | DOI: 10.1038/nature07971, PubMed: 19424153 |
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 Map |
| File |  EMD-1612.map ( map file in CCP4 format, 2050 KB ) |
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| Projections & Slices | Size of images: | Axes |  Z (Sec.) |  Y (Row.) |  X (Col.) |
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| Surface |  |  |  |
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Projections |  |  |  |
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Slices (1/3) |  |  |  |
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Slices (1/2) |  |  |  |
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Slices (2/3) |  |  |  |
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Images are generated by Spider package. |
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| Density |
| Contour Level: | 0.065 (by author), 0.065 (movie #1): |
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| Minimum - Maximum: | -0.20561 - 0.320627 |
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| Average (Standard dev.): | 0.00281696 (0.0380516) |
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|
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| Data Type | Image stored as Reals |
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| Space Group Number | 1 |
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| Map Geometry | | Axis Order : | X | Y | Z |
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| Dimensions : | 80 | 80 | 80 |
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| Origin : | 0 | 0 | 0 |
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| Limit : | 79 | 79 | 79 |
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| Spacing : | 80 | 80 | 80 |
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|
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| Unit Cell | A = 784 A , B = 784 A , C = 784 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees |
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| Pixel Spacing | X = 9.8 A , Y = 9.8 A , Z = 9.8 A |
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| CCP4 map header info | | mode | Image stored as Reals |
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| A/pix X/Y/Z | 9.8 | 9.8 | 9.8 |
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| M x/y/z | 80 | 80 | 80 |
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| origin x/y/z | 0.000 | 0.000 | 0.000 |
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| length x/y/z | 784.000 | 784.000 | 784.000 |
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| alpha/beta/gamma | 90.000 | 90.000 | 90.000 |
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| start NX/NY/NZ | -17 | -17 | -200 |
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| NX/NY/NZ | 123 | 123 | 401 |
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| MAP C/R/S | 1 | 2 | 3 |
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| start NC/NR/NS | 0 | 0 | 0 |
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| NC/NR/NS | 80 | 80 | 80 |
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| start NC,NX/NR,NY/NS,NZ | | | |
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| NC,NX/NR,NY/NS,NZ | | | |
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| D min/max/mean | -0.206 | 0.321 | 0.003 |
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|
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| Annotation Details | 3D Map of DNA Box |
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