0.025129 0.014508 0.000000 0.000000 0.029016 0.000000 0.000000 0.000000 0.016814 0.00000 0.00000 0.00000 3.54356 2.42580 25.62398 1.50364 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 4.01032 2.96436 19.97189 1.75589 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 4.49882 3.47563 15.80542 1.70748 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 9.51135 5.44231 1.42069 35.72801 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 0009-0008-5770-8014 Horvath, A. 0000-0003-1200-583X Woloszyn, K. 0000-0001-8243-650X Vecchioni, S. 0000-0001-7500-4282 Ohayon, Y.P. 0000-0002-0807-734X Sha, R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 3 90.000 90.000 120.000 39.795 39.795 59.473 81566.779 C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N O N 145 N H N 146 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing UK Nat Commun 2041-1723 17 10.1038/s41467-026-69973-1 41735315 Blunt-force assembly of programmable DNA architectures using pi-pi stacking. 2026 0009-0008-5770-8014 0000-0001-9169-1780 0000-0003-0765-9425 0000-0001-7500-4282 0000-0001-8243-650X 0000-0002-0807-734X 10.2210/pdb9q5j/pdb pdb_00009q5j 100 1 N PIXEL 2023-06-17 DECTRIS EIGER X 9M SINGLE WAVELENGTH M x-ray 1 0.920105 1.0 17-ID APS 0.920105 SYNCHROTRON APS BEAMLINE 17-ID 1511.022 DNA (5'-D(P*GP*TP*CP*TP*G)-3') 1 syn polymer 2146.449 DNA (5'-D(P*AP*GP*GP*AP*CP*TP*A)-3') 1 syn polymer 1439.988 DNA (5'-D(P*CP*AP*CP*CP*T)-3') 1 syn polymer 2137.435 DNA (5'-D(P*TP*AP*GP*TP*GP*AP*C)-3') 1 syn polymer 18.015 water 9 nat water no no (DG)(DT)(DC)(DT)(DG) GTCTG A polydeoxyribonucleotide no no (DA)(DG)(DG)(DA)(DC)(DT)(DA) AGGACTA B polydeoxyribonucleotide no no (DC)(DA)(DC)(DC)(DT) CACCT C polydeoxyribonucleotide no no (DT)(DA)(DG)(DT)(DG)(DA)(DC) TAGTGAC D polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n 1 3.76 67.27 VAPOR DIFFUSION, HANGING DROP 100 mM MOPS, 1.25 M magnesium sulfate 293 338-293 at 0.4/hr 7.333 1 19 A 7 D 11 -0.726 A_DG7:DC11_D 1 -3.990 -0.220 0.292 -0.142 2.897 1 20 A 8 D 10 -1.501 A_DT8:DA10_D 2 -10.019 -0.478 0.087 -0.164 2.060 1 19 A 9 D 9 -1.078 A_DC9:DG9_D 3 -8.700 0.196 0.295 -0.132 -7.768 1 20 A 10 C 2 2.095 A_DT10:DA2_C 4 -7.304 -0.182 -0.218 0.037 4.752 1 19 A 11 C 1 3.395 A_DG11:DC1_C 5 -5.670 -0.239 -0.029 -0.145 11.201 1 20 B 1 C 5 -6.435 B_DA1:DT5_C 6 -11.749 0.256 0.293 -0.144 8.276 1 19 B 2 C 4 -1.104 B_DG2:DC4_C 7 -10.745 -0.117 0.103 -0.049 1.436 1 19 B 3 C 3 1.515 B_DG3:DC3_C 8 -16.326 -0.206 0.040 -0.166 -1.603 1 20 B 4 D 8 -0.645 B_DA4:DT8_D 9 -9.796 0.111 -0.293 -0.166 6.749 1 19 B 5 D 7 2.507 B_DC5:DG7_D 10 -8.708 0.233 -0.045 -0.149 6.335 1 20 B 6 D 6 -8.952 B_DT6:DA6_D 11 -11.187 -0.386 -0.309 -0.334 5.354 1 20 B 7 D 5 -2.741 B_DA7:DT5_D 12 -6.360 0.266 0.225 -0.070 3.497 33.664 A A 7 8 -6.028 D D 11 10 3.386 -3.485 -0.177 -1.248 AA_DG7DT8:DA10DC11_DD 1 -0.514 0.889 33.484 -1.556 0.218 3.173 41.231 A A 8 9 -0.925 D D 10 9 3.227 -0.651 0.662 -0.595 AA_DT8DC9:DG9DA10_DD 2 -3.410 4.848 41.091 -0.776 -1.301 3.089 27.456 A A 9 10 7.146 D C 9 2 3.453 3.365 -0.743 -1.230 AA_DC9DT10:DA2DG9_CD 3 5.032 -10.686 26.793 -3.430 2.820 3.134 29.281 A A 10 11 13.274 C C 2 1 2.963 6.648 -0.261 1.054 AA_DT10DG11:DC1DA2_CC 4 -2.223 4.440 28.448 0.726 0.062 3.644 35.650 B B 1 2 -4.037 C C 5 4 3.590 -2.468 1.046 -0.080 BB_DA1DG2:DC4DT5_CC 5 2.224 -3.638 35.500 0.266 -1.351 3.329 40.897 B B 2 3 4.335 C C 4 3 3.377 3.016 -0.237 -0.549 BB_DG2DG3:DC3DC4_CC 6 -6.200 8.913 40.336 -1.127 -0.362 3.370 31.824 B B 3 4 -2.890 C D 3 8 3.357 -1.584 -0.952 -0.591 BB_DG3DA4:DT8DC3_DC 7 0.380 -0.693 31.783 -0.781 1.808 3.150 31.030 B B 4 5 4.889 D D 8 7 3.160 2.612 0.451 0.005 BB_DA4DC5:DG7DT8_DD 8 0.061 -0.114 30.922 -0.476 -0.831 3.290 40.093 B B 5 6 4.522 D D 7 6 3.269 3.096 -0.707 0.892 BB_DC5DT6:DA6DG7_DD 9 1.894 -2.767 39.935 0.946 1.248 3.301 35.232 B B 6 7 3.102 D D 6 5 3.360 1.876 0.914 -0.148 BB_DT6DA7:DT5DA6_DD 10 -1.689 2.793 35.144 -0.528 -1.766 citation citation_author repository Initial release Database references 1 0 2025-12-03 1 1 2026-05-13 _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year United States Office of Naval Research (ONR) N000141912596 United States Department of Energy (DOE, United States) DE-SC0007991 United States National Science Foundation (NSF, United States) CCF-2106790 United States National Science Foundation (NSF, United States) GCR-2317843 rs17@nyu.edu 0000-0002-0807-734X Ruojie Sha principal investigator/group leader N RCSB Y RCSB 2025-08-20 REL REL HOH water 32630 synthetic construct sample 1 5 32630 synthetic construct sample 1 7 32630 synthetic construct sample 1 5 32630 synthetic construct sample 1 7 N 8d93 PDB experimental model HOH 12 5 HOH HOH 101 A HOH 2 5 HOH HOH 102 A HOH 36 5 HOH HOH 101 B HOH 35 5 HOH HOH 102 B HOH 11 5 HOH HOH 103 B HOH 38 5 HOH HOH 101 C HOH 1 5 HOH HOH 102 C HOH 37 5 HOH HOH 103 C HOH 7 5 HOH HOH 101 D DG 7 n 1 DG 7 A DT 8 n 2 DT 8 A DC 9 n 3 DC 9 A DT 10 n 4 DT 10 A DG 11 n 5 DG 11 A DA 1 n 1 DA 1 B DG 2 n 2 DG 2 B DG 3 n 3 DG 3 B DA 4 n 4 DA 4 B DC 5 n 5 DC 5 B DT 6 n 6 DT 6 B DA 7 n 7 DA 7 B DC 1 n 1 DC 1 C DA 2 n 2 DA 2 C DC 3 n 3 DC 3 C DC 4 n 4 DC 4 C DT 5 n 5 DT 5 C DT 5 n 1 DT 5 D DA 6 n 2 DA 6 D DG 7 n 3 DG 7 D DT 8 n 4 DT 8 D DG 9 n 5 DG 9 D DA 10 n 6 DA 10 D DC 11 n 7 DC 11 D 2.80611997358 1.16874191867 2.20398280614 5.89061586861 -1.14923875569 2.51707109452 0.282050837473 -0.0179490034976 -0.101555856648 0.893937655025 -0.75406146532 0.347178197934 0.0506438494155 -0.810299977931 0.116943241785 0.448307322817 0.187159141113 -0.0163677813757 1.06778155103 -0.137331957199 0.54860984667 refined 10.3052570722 -5.06512101106 19.1114180318 X-RAY DIFFRACTION 6.61408234406 -1.54385663893 3.14799863257 4.32358130643 -3.7189189674 3.71403815118 -0.295896036863 -0.117310474195 -0.904203055723 -0.327819948988 0.332541137176 -0.071987060503 0.362229680535 0.46382958811 -0.12042376723 0.799627063664 0.284306711965 0.0921976193718 0.501609471918 -0.0648119651709 0.53978608595 refined 9.01612539183 -5.44750260878 -5.85473493649 X-RAY DIFFRACTION 3.93796579706 0.101197825648 3.44664998248 2.52005179293 1.51172389237 3.78094984562 -0.570725313599 0.130939032718 0.73067588507 -0.691773496429 -0.412555038565 0.0791148535592 -0.259099954996 0.485298938563 0.252909491157 0.304503865133 0.158420312853 0.249188989748 0.363046518426 -0.177027481772 0.329170364789 refined 6.83369659032 -1.01323880993 2.02006464753 X-RAY DIFFRACTION 5.56547457374 0.640101278179 0.689678671728 2.13507487497 1.22755220773 3.59105985732 0.0595099991353 -0.853896020881 -0.494716413038 -0.200477846991 -1.14323184251 -0.704962094777 0.920337772929 0.358723121606 -0.0353228295125 0.537169356772 0.123287612866 0.134415856582 0.505136479016 -0.0263259428159 0.492441371906 refined 11.0948945397 -6.94648293925 5.84543507441 X-RAY DIFFRACTION A 7 A A 11 A X-RAY DIFFRACTION 1 (chain 'A' and resid 7 through 11) B 1 B B 7 B X-RAY DIFFRACTION 2 (chain 'B' and resid 1 through 7) C 1 C C 5 C X-RAY DIFFRACTION 3 (chain 'C' and resid 1 through 5) D 5 D D 11 D X-RAY DIFFRACTION 4 (chain 'D' and resid 5 through 11) author_defined_assembly 12 dodecameric native gel electrophoresis 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 -0.5000000000 -0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_544 -y,x-y-1,z-1/3 crystal symmetry operation 19.8975000000 -34.4634809436 -19.8243333333 -0.5000000000 0.8660254038 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 3_655 -x+y+1,-x,z+1/3 crystal symmetry operation 39.7950000000 0.0000000000 19.8243333333 1 2.15 0.30 108.30 110.45 B B B O4' C1' N1 DC DC DC 5 5 5 N 1 -2.96 0.40 104.50 101.54 C C C O4' C4' C3' DT DT DT 5 5 5 N 1 D D O3' C3' DA DA 6 6 -0.040 0.006 1.419 1.379 N 57.87 0.2719 0.2701 0.2702 1.87 29.82 295 5871 6166 4.78 71.11 0.1426 1 FREE R-VALUE 1.96 MOLECULAR REPLACEMENT 46.7199 0.9000 1.1000 GeoStd + Monomer Library + CDL v1.2 FLAT BULK SOLVENT MODEL 1.87 29.82 9 495 0 486 0 0.0102 542 1.1914 828 0.0576 94 0.0082 24 35.2442 250 0.4202 0.4084 2.36 82 1804 43.56 0.2594 0.2585 29.82 213 4067 98.64 38.91 1.87 34.464 9Q5J 6224 0.995 1 8.2 10.5 89.4 1.873 2.063 311 0.361 1 5.659 34.464 311 0.994 1 refinement PHENIX 1.21.2_5419 data reduction autoPROC data scaling STARANISO phasing PHASER 145 trigonal P 32 P 32 x,y,z -y,x-y,z+2/3 -x+y,-x,z+1/3 N [12-5B G|A] 12 bp tensegrity triangle that propagates via blunt-end stacking with G stacking on A at the interface 1 N N 2 N N 3 N N 4 N N 5 N N 5 N N 5 N N 5 N N hydrog WATSON-CRICK A DG 7 A N1 DG 1 1_555 D DC 11 D N3 DC 7 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 1 1_555 D DC 11 D O2 DC 7 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 1 1_555 D DC 11 D N4 DC 7 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 2 1_555 D DA 10 D N1 DA 6 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 2 1_555 D DA 10 D N6 DA 6 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 3 1_555 D DG 9 D N1 DG 5 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 3 1_555 D DG 9 D O6 DG 5 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 3 1_555 D DG 9 D N2 DG 5 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 4 1_555 C DA 2 C N1 DA 2 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 4 1_555 C DA 2 C N6 DA 2 1_555 hydrog WATSON-CRICK A DG 11 A N1 DG 5 1_555 C DC 1 C N3 DC 1 1_555 hydrog WATSON-CRICK A DG 11 A N2 DG 5 1_555 C DC 1 C O2 DC 1 1_555 hydrog WATSON-CRICK A DG 11 A O6 DG 5 1_555 C DC 1 C N4 DC 1 1_555 hydrog WATSON-CRICK B DA 1 B N1 DA 1 1_555 C DT 5 C N3 DT 5 1_555 hydrog WATSON-CRICK B DA 1 B N6 DA 1 1_555 C DT 5 C O4 DT 5 1_555 hydrog WATSON-CRICK B DG 2 B N1 DG 2 1_555 C DC 4 C N3 DC 4 1_555 hydrog WATSON-CRICK B DG 2 B N2 DG 2 1_555 C DC 4 C O2 DC 4 1_555 hydrog WATSON-CRICK B DG 2 B O6 DG 2 1_555 C DC 4 C N4 DC 4 1_555 hydrog WATSON-CRICK B DG 3 B N1 DG 3 1_555 C DC 3 C N3 DC 3 1_555 hydrog WATSON-CRICK B DG 3 B N2 DG 3 1_555 C DC 3 C O2 DC 3 1_555 hydrog WATSON-CRICK B DG 3 B O6 DG 3 1_555 C DC 3 C N4 DC 3 1_555 hydrog WATSON-CRICK B DA 4 B N1 DA 4 1_555 D DT 8 D N3 DT 4 1_555 hydrog WATSON-CRICK B DA 4 B N6 DA 4 1_555 D DT 8 D O4 DT 4 1_555 hydrog WATSON-CRICK B DC 5 B N3 DC 5 1_555 D DG 7 D N1 DG 3 1_555 hydrog WATSON-CRICK B DC 5 B N4 DC 5 1_555 D DG 7 D O6 DG 3 1_555 hydrog WATSON-CRICK B DC 5 B O2 DC 5 1_555 D DG 7 D N2 DG 3 1_555 hydrog WATSON-CRICK B DT 6 B N3 DT 6 1_555 D DA 6 D N1 DA 2 1_555 hydrog WATSON-CRICK B DT 6 B O4 DT 6 1_555 D DA 6 D N6 DA 2 1_555 hydrog WATSON-CRICK B DA 7 B N1 DA 7 1_555 D DT 5 D N3 DT 1 1_555 hydrog WATSON-CRICK B DA 7 B N6 DA 7 1_555 D DT 5 D O4 DT 1 1_555 DNA dna, tensegrity triangle, stacking, blunt 9Q5J PDB 1 1 9Q5J 9Q5J PDB 2 1 9Q5J 9Q5J PDB 3 1 9Q5J 9Q5J PDB 4 1 9Q5J 7 11 9Q5J 7 11 9Q5J A 1 1 5 1 7 9Q5J 1 7 9Q5J B 2 1 7 1 5 9Q5J 1 5 9Q5J C 3 1 5 5 11 9Q5J 5 11 9Q5J D 4 1 7 145 P 32 P 32