0.028683 0.000000 0.000000 0.000000 0.028683 0.000000 0.000000 0.000000 0.009689 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. 0000-0002-6692-3532 Singh, V.R. 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 4 90.000 90.000 90.000 34.864 34.864 103.212 125454.031 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 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 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 To Be Published 0353 Mobile Junction in Double Crossover-Like Tiles 0009-0008-5770-8014 0000-0001-8243-650X 0000-0001-7500-4282 0000-0002-0807-734X 10.2210/pdb9ybj/pdb pdb_00009ybj 100 1 N PIXEL 2024-12-13 DECTRIS EIGER X 9M SINGLE WAVELENGTH M x-ray 1 0.92021 1.0 17-ID APS 0.92021 SYNCHROTRON APS BEAMLINE 17-ID 4930.189 DNA (5'-D(*TP*GP*AP*CP*GP*GP*CP*TP*GP*GP*AP*CP*TP*CP*G)-3') 1 syn polymer 4868.169 DNA (5'-D(*CP*AP*AP*GP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*C)-3') 1 syn polymer no no (DT)(DG)(DA)(DC)(DG)(DG)(DC)(DT)(DG)(DG)(DA)(DC)(DT)(DC)(DG)(DT) TGACGGCTGGACTCGT A polydeoxyribonucleotide no no (DC)(DA)(DA)(DG)(DC)(DC)(DG)(DT)(DG)(DA)(DG)(DT)(DC)(DC)(DA)(DC) CAAGCCGTGAGTCCAC B 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 n n n n n n n n 1 3.20 61.57 VAPOR DIFFUSION, HANGING DROP 100 mM MOPS, 1.25 M magnesium sulfate 293 338-293 at 0.4/hr -3.638 1 20 A 3 B 8 -0.198 A_DA3:DT8_B 1 -5.407 0.080 0.074 -0.094 -3.259 1 19 A 4 B 7 0.381 A_DC4:DG7_B 2 -5.213 0.197 0.136 -0.127 -6.562 1 19 A 5 B 6 1.909 A_DG5:DC6_B 3 2.173 -0.226 -0.338 -0.184 -1.368 1 19 A 6 B 5 0.380 A_DG6:DC5_B 4 -1.132 -0.214 0.134 -0.103 0.014 1 19 A 7 B 4 -1.051 A_DC7:DG4_B 5 -2.916 0.202 0.357 -0.163 -2.451 1 20 A 8 B 15 3.136 A_DT8:DA15_B 6 -7.344 -0.106 0.202 -0.171 0.997 1 19 A 9 B 14 0.502 A_DG9:DC14_B 7 -1.716 -0.223 0.287 -0.148 4.174 1 19 A 10 B 13 1.261 A_DG10:DC13_B 8 1.215 -0.203 0.257 -0.150 3.133 1 20 A 11 B 12 2.363 A_DA11:DT12_B 9 -3.309 0.092 0.185 -0.137 0.594 1 19 A 12 B 11 1.071 A_DC12:DG11_B 10 -5.201 0.206 0.085 -0.150 -3.996 1 20 A 13 B 10 2.732 A_DT13:DA10_B 11 -6.218 -0.101 0.177 -0.168 -4.930 1 19 A 14 B 9 0.919 A_DC14:DG9_B 12 -0.223 0.213 0.171 -0.141 3.283 31.354 A A 3 4 2.615 B B 8 7 3.312 1.412 -0.165 -0.674 AA_DA3DC4:DG7DT8_BB 1 -1.605 2.971 31.283 -1.515 0.000 3.625 33.622 A A 4 5 0.573 B B 7 6 3.539 0.330 0.772 1.014 AA_DC4DG5:DC6DG7_BB 2 5.277 -9.159 33.215 1.694 -0.385 3.460 34.807 A A 5 6 8.634 B B 6 5 3.269 5.104 -0.997 0.594 AA_DG5DG6:DC5DC6_BB 3 -7.995 13.526 33.528 0.178 0.390 3.075 35.857 A A 6 7 6.398 B B 5 4 3.161 3.931 0.366 -0.596 AA_DG6DC7:DG4DC5_BB 4 -0.450 0.733 35.645 -1.507 -0.656 3.527 37.698 A A 8 9 5.744 B B 15 14 3.490 3.705 0.336 0.440 AA_DT8DG9:DC14DA15_BB 5 1.518 -2.353 37.492 0.166 -0.309 3.263 29.264 A A 9 10 6.528 B B 14 13 3.287 3.291 0.083 -0.029 AA_DG9DG10:DC13DC14_BB 6 -0.353 0.699 29.080 -0.773 -0.240 3.337 36.912 A A 10 11 1.319 B B 13 12 3.316 0.834 -0.489 -0.219 AA_DG10DA11:DT12DC13_BB 7 -2.737 4.327 36.804 -0.461 0.395 3.386 34.355 A A 11 12 -2.470 B B 12 11 3.342 -1.458 0.280 -1.121 AA_DA11DC12:DG11DT12_BB 8 0.020 -0.033 34.325 -1.664 -0.471 3.459 31.230 A A 12 13 -3.110 B B 11 10 3.418 -1.674 -0.054 -0.925 AA_DC12DT13:DA10DG11_BB 9 0.695 -1.293 31.178 -1.383 0.240 3.254 37.457 A A 13 14 1.372 B B 10 9 3.264 0.881 -0.122 -0.513 AA_DT13DC14:DG9DA10_BB 10 -1.013 1.578 37.434 -0.913 0.057 repository Initial release 1 0 2025-10-22 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 2025-09-17 REL REL 32630 synthetic construct sample 1 16 32630 synthetic construct sample 1 16 N 8epf PDB experimental model DT 1 n 1 DT 1 A DG 2 n 2 DG 2 A DA 3 n 3 DA 3 A DC 4 n 4 DC 4 A DG 5 n 5 DG 5 A DG 6 n 6 DG 6 A DC 7 n 7 DC 7 A DT 8 n 8 DT 8 A DG 9 n 9 DG 9 A DG 10 n 10 DG 10 A DA 11 n 11 DA 11 A DC 12 n 12 DC 12 A DT 13 n 13 DT 13 A DC 14 n 14 DC 14 A DG 15 n 15 DG 15 A DT 16 n 16 DT 16 A DC 1 n 1 DC 1 B DA 2 n 2 DA 2 B DA 3 n 3 DA 3 B DG 4 n 4 DG 4 B DC 5 n 5 DC 5 B DC 6 n 6 DC 6 B DG 7 n 7 DG 7 B DT 8 n 8 DT 8 B DG 9 n 9 DG 9 B DA 10 n 10 DA 10 B DG 11 n 11 DG 11 B DT 12 n 12 DT 12 B DC 13 n 13 DC 13 B DC 14 n 14 DC 14 B DA 15 n 15 DA 15 B DC 16 n 16 DC 16 B 1.24442072953 0.833939213824 -0.255520948132 1.14315717539 -0.847381261273 1.67776931166 0.539650338405 0.61745433983 0.284077819533 -0.483668015419 0.790416854805 0.40161700432 0.0512075184818 0.0764521287859 3.55228703001 0.175515191527 -0.187248888662 0.103248946094 0.524292793775 -0.107942671669 0.315984343259 refined 7.43820751597 -7.72553342247 -3.2319458268 X-RAY DIFFRACTION 1.15158359095 0.855604288852 -0.555971133455 1.81100100487 0.311770650682 1.86831940247 0.225979636842 0.480547120949 0.5209387334 0.799032113276 0.796952002568 0.0010129257371 0.24442221345 -0.192541081492 1.7755208727 0.154429025827 -0.138897443289 -0.0476144606029 0.214995473778 -0.00790832251662 0.224901823529 refined 7.24226119253 -9.2505079024 2.77830904491 X-RAY DIFFRACTION A 1 A A 16 A X-RAY DIFFRACTION 1 (chain 'A' and resid 1 through 16) B 1 B B 16 B X-RAY DIFFRACTION 2 (chain 'B' and resid 1 through 16) author_and_software_defined_assembly PISA 2 dimeric native gel electrophoresis 1160 -9 6500 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 51.68 0.2847 0.2673 0.2680 2.14 33.03 153 3179 3332 4.59 49.14 0.2926 1 FREE R-VALUE 1.34 MOLECULAR REPLACEMENT 34.1292 0.9000 1.1000 GeoStd + Monomer Library + CDL v1.2 FLAT BULK SOLVENT MODEL 2.14 33.03 0 650 0 650 0 0.0039 728 0.6025 1120 0.0327 126 0.0033 32 34.8571 336 0.2847 0.2673 33.03 153 3179 49.14 2.14 33.03 9YBJ 3349 0.969 1 12.2 8.9 83.6 2.142 2.454 197 0.448 1 6.957 33.030 197 0.858 1 refinement PHENIX 1.21.2_5419 data reduction autoPROC data scaling STARANISO phasing PHASER 78 tetragonal P 43 P 4cw x,y,z -y,x,z+3/4 y,-x,z+1/4 -x,-y,z+1/2 N [2UDS] Double crossover-like DNA motif containing a mobile junction 1 N N 2 N N hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 8 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 8 B O4 DT 8 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 B DG 7 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 B DG 7 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 B DG 7 B N2 DG 7 1_555 hydrog WATSON-CRICK A DG 5 A N1 DG 5 1_555 B DC 6 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 B DC 6 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 B DC 6 B N4 DC 6 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 5 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 5 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 5 B N4 DC 5 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B DG 4 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B DG 4 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B DG 4 B N2 DG 4 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 15 B N1 DA 15 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 15 B N6 DA 15 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B DC 14 B N3 DC 14 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B DC 14 B O2 DC 14 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B DC 14 B N4 DC 14 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 13 B N3 DC 13 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 13 B O2 DC 13 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 13 B N4 DC 13 1_555 hydrog WATSON-CRICK A DA 11 A N1 DA 11 1_555 B DT 12 B N3 DT 12 1_555 hydrog WATSON-CRICK A DA 11 A N6 DA 11 1_555 B DT 12 B O4 DT 12 1_555 hydrog WATSON-CRICK A DC 12 A N3 DC 12 1_555 B DG 11 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 12 A N4 DC 12 1_555 B DG 11 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 12 A O2 DC 12 1_555 B DG 11 B N2 DG 11 1_555 hydrog WATSON-CRICK A DT 13 A N3 DT 13 1_555 B DA 10 B N1 DA 10 1_555 hydrog WATSON-CRICK A DT 13 A O4 DT 13 1_555 B DA 10 B N6 DA 10 1_555 hydrog WATSON-CRICK A DC 14 A N3 DC 14 1_555 B DG 9 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 14 A N4 DC 14 1_555 B DG 9 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 14 A O2 DC 14 1_555 B DG 9 B N2 DG 9 1_555 DNA dna, dxl, crossover, mobile 9YBJ PDB 1 1 9YBJ 9YBJ PDB 2 1 9YBJ 1 16 9YBJ 1 16 9YBJ A 1 1 16 1 16 9YBJ 1 16 9YBJ B 2 1 16 78 P 43 P 4cw