0.023856 0.013773 0.000000 0.000000 0.027546 0.000000 0.000000 0.000000 0.014610 0.000000 0.000000 0.000000 Ovaere, M. Van Meervelt, L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.000 90.000 120.000 41.919 41.919 68.444 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer Mg 2 24.305 MAGNESIUM ION non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking C12 H16 N5 O5 P 341.260 [(1R,4S,6S)-4-(6-AMINO-9H-PURIN-9-YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN PHOSPHATE DNA linking C11 H16 N3 O6 P 317.235 n [(1R,4S,6S)-4-(4-amino-2-oxopyrimidin-1(2H)-yl)-6-hydroxycyclohex-2-en-1-yl]methyl dihydrogen phosphate DNA linking C12 H16 N5 O6 P 357.259 n [(1R,4S,6S)-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-6-hydroxycyclohex-2-en-1-yl]methyl dihydrogen phosphate DNA linking C12 H17 N2 O7 P 332.246 n [(1R,4S,6S)-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclohex-2-en-1-yl]methyl dihydrogen phosphate 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 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C 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 H N 38 N O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 R C N 49 N O N 50 R C N 51 N N N 52 N C N 53 N O N 54 N N N 55 N C N 56 N N N 57 N C N 58 N C 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 H N 72 N H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 N C N 84 R C N 85 N N N 86 N C N 87 N O N 88 N N N 89 N C N 90 N O N 91 N C N 92 N C N 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 H N 109 N O N 110 N P N 111 N O N 112 N O N 113 N O N 114 N C N 115 R C N 116 N O N 117 S C N 118 N O N 119 R C N 120 N O N 121 R C Y 122 N N Y 123 N C Y 124 N N Y 125 N C N 126 N C N 127 N O N 128 N N N 129 N C N 130 N N N 131 N N Y 132 N C 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 H N 145 N H N 146 N H N 147 N O N 148 N H N 149 N H N 150 N MG N 151 N O N 152 N P N 153 N O N 154 N O N 155 N O N 156 N C N 157 R C N 158 N O N 159 S C N 160 N O N 161 R C N 162 N O N 163 R C N 164 N N N 165 N C N 166 N O N 167 N N N 168 N C N 169 N O N 170 N C N 171 N C N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N O N 186 N O N 187 N P N 188 N O N 189 N O N 190 N C N 191 R C N 192 S C N 193 N O N 194 N C N 195 S C N 196 N C N 197 N C Y 198 N N Y 199 N C Y 200 N N Y 201 N C Y 202 N C Y 203 N N Y 204 N C N 205 N N Y 206 N N Y 207 N C N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N P N 225 N N N 226 N C N 227 N O N 228 N N N 229 N C N 230 N N N 231 N C N 232 N C N 233 S C N 234 N C N 235 S C N 236 N O N 237 R C N 238 N C N 239 N O N 240 N C N 241 N C N 242 N O N 243 N O N 244 N O N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N P N 262 N N N 263 N C N 264 N N N 265 N N Y 266 N C Y 267 N C N 268 N C N 269 N O Y 270 N N Y 271 N C Y 272 N N N 273 S C N 274 N C N 275 S C N 276 N O N 277 R C N 278 N C N 279 N O N 280 N C N 281 N C N 282 N O N 283 N O N 284 N O N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N H N 296 N H N 297 N H N 298 N H N 299 N H N 300 N H N 301 N O N 302 R C N 303 N C N 304 N C N 305 S C N 306 N O N 307 N C N 308 N C N 309 N C N 310 N C N 311 N N N 312 N C N 313 N O N 314 N N N 315 N C N 316 S C N 317 N P N 318 N O N 319 N O N 320 N O N 321 N C N 322 N O N 323 N H N 324 N H N 325 N H N 326 N H N 327 N H N 328 N H N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N H N 335 N H N 336 N H N 337 N H N 338 N H N 339 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 N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing N 41 N sing N 42 N doub 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 sing N 65 N sing N 66 N doub N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub 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 N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N doub N 102 N sing N 103 N sing N 104 N sing N 105 N doub N 106 N sing N 107 N sing N 108 N doub N 109 N sing 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 Y 137 N sing Y 138 N sing Y 139 N doub N 140 N sing Y 141 N sing N 142 N sing Y 143 N doub N 144 N doub N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N doub N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N doub N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N doub N 182 N sing N 183 N sing N 184 N sing N 185 N doub N 186 N sing N 187 N doub N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N doub N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N doub N 214 N sing N 215 N sing Y 216 N sing Y 217 N sing Y 218 N doub N 219 N sing Y 220 N sing Y 221 N doub Y 222 N sing Y 223 N sing Y 224 N doub Y 225 N doub N 226 N sing N 227 N sing N 228 N sing Y 229 N sing N 230 N sing N 231 N doub N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N doub N 240 N doub N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N doub N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N doub N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N doub N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N doub N 278 N sing N 279 N sing N 280 N sing Y 281 N doub Y 282 N sing N 283 N sing Y 284 N sing N 285 N doub Y 286 N doub Y 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N doub N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N doub N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N doub N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N doub N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N doub N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N doub N 342 N sing N 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing GE Chemistry 0947-6539 17 7823 7830 10.1002/chem.201003594 21618623 The Crystal Structure of the CeNA:RNA Hybrid ce(GCGTAGCG):r(CGCUACGC). 2011 10.2210/pdb3knc/pdb pdb_00003knc 100 1 CCD 2008-09-29 MARMOSAIC 225 mm CCD SINGLE WAVELENGTH M x-ray 1 1.0000 1.0 X06DA SLS 1.0000 SYNCHROTRON SLS BEAMLINE X06DA CeNA 2887.177 5'-D(*(XGR)P*(XCR)P*(XGR)P*(XTR)P*(XAR)P*(XGR)P*(XCR)P*(XGR)P*(XGR))-3' 1 syn polymer RNA 2501.553 5'-R(*CP*GP*CP*UP*AP*CP*GP*C)-3' 1 syn polymer 24.305 MAGNESIUM ION 2 syn non-polymer 18.015 water 47 nat water no yes (XGR)(XCR)(XGR)(XTR)(XAR)(XGR)(XCR)(XGR)(XGR) GCGTNGCGG A polydeoxyribonucleotide no no CGCUACGC CGCUACGC B polyribonucleotide n n n n n n n n n n n n n n n n n 1 3.22 61.82 The structure factor file contains Friedel pairs VAPOR DIFFUSION, HANGING DROP 0.2M Magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 289K 289 Magnesium formate 1 Magnesium formate 2 1.753 1 19 A 1 B 8 1.052 A_XGR1:C8_B 1 -12.277 0.061 0.545 -0.125 -5.102 1 19 A 2 B 7 1.030 A_XCR2:G7_B 2 -12.505 0.005 0.521 -0.244 -9.561 1 19 A 3 B 6 5.729 A_XGR3:C6_B 3 -14.167 -0.165 0.317 0.080 -8.304 1 20 A 4 B 5 -2.908 A_XTR4:A5_B 4 -13.046 0.375 0.439 -0.121 -2.720 1 19 A 6 B 3 -5.217 A_XGR6:C3_B 5 -11.560 -0.063 -0.065 -0.279 -3.273 1 19 A 7 B 2 0.859 A_XCR7:G2_B 6 -10.283 -0.466 0.191 -0.086 -9.236 1 19 A 8 B 1 5.307 A_XGR8:C1_B 7 -15.039 -0.473 -0.252 0.018 3.065 35.251 A A 1 2 5.050 B B 8 7 3.270 3.054 -0.159 -2.349 AA_XGR1XCR2:G7C8_BB 1 -1.344 2.222 35.098 -4.319 0.069 2.487 32.155 A A 2 3 15.881 B B 7 6 3.125 8.686 -0.151 -1.941 AA_XCR2XGR3:C6G7_BB 2 2.134 -3.901 30.917 -4.865 0.607 2.787 36.317 A A 3 4 10.348 B B 6 5 3.143 6.416 -0.415 -1.691 AA_XGR3XTR4:A5C6_BB 3 1.632 -2.631 35.729 -3.532 0.874 3.873 65.770 A A 4 6 27.077 B B 5 3 5.819 28.602 0.181 -3.741 AA_XTR4XGR6:C3A5_BB 4 3.937 -3.727 59.744 -5.281 0.086 2.983 29.035 A A 6 7 10.479 B B 3 2 3.382 5.223 0.957 -2.249 AA_XGR6XCR7:G2C3_BB 5 1.749 -3.508 28.518 -5.613 -1.531 2.029 32.941 A A 7 8 25.197 B B 2 1 3.246 13.860 -0.250 -2.222 AA_XCR7XGR8:C1G2_BB 6 1.636 -2.974 29.913 -5.921 0.678 software database_2 pdbx_struct_conn_angle struct_conn struct_ref_seq struct_ref_seq_dif struct_site chem_comp_atom chem_comp_bond repository Initial release Version format compliance Other Refinement description Database references Derived calculations Data collection 1 0 2010-12-08 1 1 2011-07-13 1 2 2012-02-01 1 3 2017-11-01 1 4 2021-10-13 1 5 2024-02-21 _software.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr2_auth_seq_id _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2009-11-12 REL REL MG MAGNESIUM ION HOH water The CeNA strand was synthesized. sample The RNA strand was synthesized. sample MG 100 3 MG MG 100 A MG 200 3 MG MG 200 A HOH 14 4 HOH HOH 14 A HOH 15 4 HOH HOH 15 A HOH 17 4 HOH HOH 17 A HOH 20 4 HOH HOH 20 A HOH 22 4 HOH HOH 22 A HOH 23 4 HOH HOH 23 A HOH 24 4 HOH HOH 24 A HOH 25 4 HOH HOH 25 A HOH 28 4 HOH HOH 28 A HOH 33 4 HOH HOH 33 A HOH 34 4 HOH HOH 34 A HOH 35 4 HOH HOH 35 A HOH 101 4 HOH HOH 101 A HOH 102 4 HOH HOH 102 A HOH 103 4 HOH HOH 103 A HOH 104 4 HOH HOH 104 A HOH 105 4 HOH HOH 105 A HOH 106 4 HOH HOH 106 A HOH 1 4 HOH HOH 107 A HOH 3 4 HOH HOH 108 A HOH 4 4 HOH HOH 109 A HOH 7 4 HOH HOH 110 A HOH 8 4 HOH HOH 111 A HOH 201 4 HOH HOH 201 A HOH 202 4 HOH HOH 202 A HOH 203 4 HOH HOH 203 A HOH 204 4 HOH HOH 204 A HOH 205 4 HOH HOH 205 A HOH 206 4 HOH HOH 206 A HOH 9 4 HOH HOH 9 B HOH 10 4 HOH HOH 10 B HOH 11 4 HOH HOH 11 B HOH 12 4 HOH HOH 12 B HOH 13 4 HOH HOH 13 B HOH 2 4 HOH HOH 14 B HOH 5 4 HOH HOH 15 B HOH 16 4 HOH HOH 16 B HOH 6 4 HOH HOH 17 B HOH 18 4 HOH HOH 18 B HOH 19 4 HOH HOH 19 B HOH 21 4 HOH HOH 21 B HOH 26 4 HOH HOH 26 B HOH 27 4 HOH HOH 27 B HOH 29 4 HOH HOH 29 B HOH 30 4 HOH HOH 30 B HOH 31 4 HOH HOH 31 B HOH 32 4 HOH HOH 32 B 31.370 2.500 2.500 24.900 24.900 Phaser MODE: MR_AUTO XGR 1 n 1 XGR 1 A XCR 2 n 2 XCR 2 A XGR 3 n 3 XGR 3 A XTR 4 n 4 XTR 4 A XAR 5 n 5 XAR 5 A XGR 6 n 6 XGR 6 A XCR 7 n 7 XCR 7 A XGR 8 n 8 XGR 8 A XGR 9 n 9 XGR 9 A C 1 n 1 C 1 B G 2 n 2 G 2 B C 3 n 3 C 3 B U 4 n 4 U 4 B A 5 n 5 A 5 B C 6 n 6 C 6 B G 7 n 7 G 7 B C 8 n 8 C 8 B author_and_software_defined_assembly PISA 2 dimeric 1280 -34.1 11444 A HOH 101 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 102 E O HOH 1_555 176.6 A HOH 101 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 103 E O HOH 1_555 92.0 A HOH 102 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 103 E O HOH 1_555 86.0 A HOH 101 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 104 E O HOH 1_555 92.6 A HOH 102 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 104 E O HOH 1_555 90.0 A HOH 103 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 104 E O HOH 1_555 90.3 A HOH 101 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 105 E O HOH 1_555 90.9 A HOH 102 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 105 E O HOH 1_555 86.5 A HOH 103 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 105 E O HOH 1_555 90.9 A HOH 104 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 105 E O HOH 1_555 176.2 A HOH 101 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 106 E O HOH 1_555 86.1 A HOH 102 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 106 E O HOH 1_555 96.1 A HOH 103 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 106 E O HOH 1_555 177.4 A HOH 104 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 106 E O HOH 1_555 88.1 A HOH 105 E O HOH 1_555 A MG 100 C MG MG 1_555 A HOH 106 E O HOH 1_555 90.8 A HOH 201 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 202 E O HOH 1_555 179.4 A HOH 201 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 203 E O HOH 1_555 89.5 A HOH 202 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 203 E O HOH 1_555 90.0 A HOH 201 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 204 E O HOH 1_555 90.8 A HOH 202 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 204 E O HOH 1_555 88.8 A HOH 203 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 204 E O HOH 1_555 88.5 A HOH 201 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 205 E O HOH 1_555 89.1 A HOH 202 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 205 E O HOH 1_555 91.3 A HOH 203 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 205 E O HOH 1_555 92.6 A HOH 204 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 205 E O HOH 1_555 178.9 A HOH 201 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 206 E O HOH 1_555 93.2 A HOH 202 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 206 E O HOH 1_555 87.2 A HOH 203 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 206 E O HOH 1_555 176.4 A HOH 204 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 206 E O HOH 1_555 89.0 A HOH 205 E O HOH 1_555 A MG 200 D MG MG 1_555 A HOH 206 E O HOH 1_555 89.9 A XGR 1 A XGR 1 DG A XCR 2 A XCR 2 DC A XGR 3 A XGR 3 DG A XTR 4 A XTR 4 DT A XGR 6 A XGR 6 DG A XCR 7 A XCR 7 DC A XGR 8 A XGR 8 DG A XGR 9 A XGR 9 DG 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 1 A MG 200 D MG 1 A N1 XGR 9 A N1 XGR 9 1 Y 1 A C2 XGR 9 A C2 XGR 9 1 Y 1 A N2 XGR 9 A N2 XGR 9 1 Y 1 A N3 XGR 9 A N3 XGR 9 1 Y 1 A C4 XGR 9 A C4 XGR 9 1 Y 1 A C5 XGR 9 A C5 XGR 9 1 Y 1 A C6 XGR 9 A C6 XGR 9 1 Y 1 A O6 XGR 9 A O6 XGR 9 1 Y 1 A N7 XGR 9 A N7 XGR 9 1 Y 1 A C8 XGR 9 A C8 XGR 9 1 Y 1 A N9 XGR 9 A N9 XGR 9 1 Y 1 A C1' XGR 9 A C1' XGR 9 1 Y 1 A C2' XGR 9 A C2' XGR 9 1 Y 1 A C3' XGR 9 A C3' XGR 9 1 Y 1 A O3' XGR 9 A O3' XGR 9 1 Y 1 A C4' XGR 9 A C4' XGR 9 1 Y 1 A C5' XGR 9 A C5' XGR 9 1 Y 1 A C6' XGR 9 A C6' XGR 9 1 Y 1 A C7' XGR 9 A C7' XGR 9 1 Y 1 B B C5' C4' U U 4 4 -0.043 0.007 1.508 1.465 N 83.75 61.046 37.01 4.490 2.240 0.000 4.490 0.000 -6.730 0.970 0.958 The Friedel pairs were used in phasing 0.232 0.184 0.187 2.50 36.3 114 2574 4.400 98.020 0.232 0.184 1.00 0.50 0.762 9.838 0.190 0.310 0.237 RANDOM 1 THROUGHOUT 0.00 MOLECULAR REPLACEMENT 0.310 0.237 0.800 0.800 1.400 MAXIMUM LIKELIHOOD BABINET MODEL WITH MASK 2.50 36.3 47 390 2 341 0 0.018 0.021 396 2.247 2.972 617 0.120 0.200 63 0.010 0.017 199 0.108 1.500 1 2.812 3.000 392 4.317 4.500 605 0.733 0.379 2.57 9 169 178 20 97.270 2.50 36.3 3KNC 2460 2575 0.048 1 9.400 98.800 data reduction Andrew G.W. Leslie andrew@mrc-lmb.cam.ac.uk http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ MOSFLM package data scaling Phil R. Evans pre@mrc-lmb.cam.ac.uk 2008/10/21 Fortran_77 http://www.ccp4.ac.uk/dist/html/scala.html SCALA other 3.3.9 phasing Randy J. Read cimr-phaser@lists.cam.ac.uk Thu Nov 13 11:40:59 2008 http://www-structmed.cimr.cam.ac.uk/phaser/ PHASER program 2.1.4 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program data extraction PDB help@deposit.rcsb.org June 11, 2008 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.005 data collection MAR345 CCD Crystal structure of the CeNA-RNA hybrid octamer ce(GCGTAGCG):r(CGCUACGC) 1 N N 2 N N 3 N N 3 N N 4 N N 4 N N Biological unit is the same as asymmetric unit covale 1.572 both A XTR 4 A O3' XTR 4 1_555 A XAR 5 A P XAR 5 1_555 metalc 2.136 A MG 100 C MG MG 1_555 A HOH 101 E O HOH 1_555 metalc 2.134 A MG 100 C MG MG 1_555 A HOH 102 E O HOH 1_555 metalc 2.130 A MG 100 C MG MG 1_555 A HOH 103 E O HOH 1_555 metalc 2.146 A MG 100 C MG MG 1_555 A HOH 104 E O HOH 1_555 metalc 2.137 A MG 100 C MG MG 1_555 A HOH 105 E O HOH 1_555 metalc 2.141 A MG 100 C MG MG 1_555 A HOH 106 E O HOH 1_555 metalc 2.160 A MG 200 D MG MG 1_555 A HOH 201 E O HOH 1_555 metalc 2.172 A MG 200 D MG MG 1_555 A HOH 202 E O HOH 1_555 metalc 2.176 A MG 200 D MG MG 1_555 A HOH 203 E O HOH 1_555 metalc 2.160 A MG 200 D MG MG 1_555 A HOH 204 E O HOH 1_555 metalc 2.164 A MG 200 D MG MG 1_555 A HOH 205 E O HOH 1_555 metalc 2.163 A MG 200 D MG MG 1_555 A HOH 206 E O HOH 1_555 hydrog WATSON-CRICK A XGR 1 A N1 XGR 1 1_555 B C 8 B N3 C 8 1_555 hydrog WATSON-CRICK A XGR 1 A N2 XGR 1 1_555 B C 8 B O2 C 8 1_555 hydrog WATSON-CRICK A XGR 1 A O6 XGR 1 1_555 B C 8 B N4 C 8 1_555 hydrog WATSON-CRICK A XCR 2 A N3 XCR 2 1_555 B G 7 B N1 G 7 1_555 hydrog WATSON-CRICK A XCR 2 A N4 XCR 2 1_555 B G 7 B O6 G 7 1_555 hydrog WATSON-CRICK A XCR 2 A O2 XCR 2 1_555 B G 7 B N2 G 7 1_555 hydrog WATSON-CRICK A XGR 3 A N1 XGR 3 1_555 B C 6 B N3 C 6 1_555 hydrog WATSON-CRICK A XGR 3 A N2 XGR 3 1_555 B C 6 B O2 C 6 1_555 hydrog WATSON-CRICK A XGR 3 A O6 XGR 3 1_555 B C 6 B N4 C 6 1_555 hydrog WATSON-CRICK A XTR 4 A N3 XTR 4 1_555 B A 5 B N1 A 5 1_555 hydrog WATSON-CRICK A XTR 4 A O4 XTR 4 1_555 B A 5 B N6 A 5 1_555 hydrog WATSON-CRICK A XGR 6 A N1 XGR 6 1_555 B C 3 B N3 C 3 1_555 hydrog WATSON-CRICK A XGR 6 A N2 XGR 6 1_555 B C 3 B O2 C 3 1_555 hydrog WATSON-CRICK A XGR 6 A O6 XGR 6 1_555 B C 3 B N4 C 3 1_555 hydrog WATSON-CRICK A XCR 7 A N3 XCR 7 1_555 B G 2 B N1 G 2 1_555 hydrog WATSON-CRICK A XCR 7 A N4 XCR 7 1_555 B G 2 B O6 G 2 1_555 hydrog WATSON-CRICK A XCR 7 A O2 XCR 7 1_555 B G 2 B N2 G 2 1_555 hydrog WATSON-CRICK A XGR 8 A N1 XGR 8 1_555 B C 1 B N3 C 1 1_555 hydrog WATSON-CRICK A XGR 8 A N2 XGR 8 1_555 B C 1 B O2 C 1 1_555 hydrog WATSON-CRICK A XGR 8 A O6 XGR 8 1_555 B C 1 B N4 C 1 1_555 RNA/CYCLOHEXENE-RNA HYBRID cyclohexene, sugar modification, RNA, RNA-CYCLOHEXENE-RNA HYBRID complex 3KNC PDB 1 1 3KNC GCGTAGCGG 3KNC PDB 2 1 3KNC CGCUACGC 1 9 3KNC 1 9 3KNC A 1 1 9 1 8 3KNC 1 8 3KNC B 2 1 8 1 C engineered mutation XGR 1 3KNC A 3KNC PDB 2 1 1 G engineered mutation XCR 2 3KNC A 3KNC PDB 3 2 1 DT engineered mutation XGR 3 3KNC A 3KNC PDB 4 3 1 A engineered mutation XTR 4 3KNC A 3KNC PDB 5 4 1 G engineered mutation XAR 5 3KNC A 3KNC PDB 6 5 1 C engineered mutation XGR 6 3KNC A 3KNC PDB 7 6 1 G engineered mutation XCR 7 3KNC A 3KNC PDB 8 7 1 G engineered mutation XGR 8 3KNC A 3KNC PDB 9 8 1 G engineered mutation XGR 9 3KNC A 3KNC PDB 10 9 BINDING SITE FOR RESIDUE MG A 100 A MG 100 Software 6 BINDING SITE FOR RESIDUE MG A 200 A MG 200 Software 12 A HOH 101 E HOH 6 1_555 A HOH 102 E HOH 6 1_555 A HOH 103 E HOH 6 1_555 A HOH 104 E HOH 6 1_555 A HOH 105 E HOH 6 1_555 A HOH 106 E HOH 6 1_555 A HOH 201 E HOH 12 1_555 A HOH 201 E HOH 12 5_555 A HOH 202 E HOH 12 1_555 A HOH 202 E HOH 12 5_555 A HOH 203 E HOH 12 1_555 A HOH 203 E HOH 12 5_555 A HOH 204 E HOH 12 5_555 A HOH 204 E HOH 12 1_555 A HOH 205 E HOH 12 5_555 A HOH 205 E HOH 12 1_555 A HOH 206 E HOH 12 5_555 A HOH 206 E HOH 12 1_555 154 P 32 2 1