0.018835 0.000000 0.007780 0.000000 0.018701 0.000000 0.000000 0.000000 0.019395 0.00000 0.00000 0.00000 6 6 2.3103 1.0201 1.5888 0.8651 20.8439 10.2075 0.5687 51.6512 0.2156 1 1 0.4930 0.3229 0.1402 0.0408 10.5109 26.1257 3.1424 57.7997 0.0030 7 7 12.2220 3.1346 2.0141 1.1672 0.0057 9.8933 28.9975 0.5826 -11.5379 8 8 3.0487 2.2870 1.5464 0.8671 13.2771 5.7011 0.3239 32.9089 0.2508 16 16 6.9054 5.2035 1.4379 1.5863 1.4679 22.2151 0.2536 56.1720 1.0220 0000-0002-8794-1385 Wei, K.Y. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90 112.443 90 53.093 53.473 55.786 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O 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 H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O 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 H N 74 N N N 75 S C N 76 N C N 77 N O N 78 N C N 79 N C N 80 N C N 81 N O N 82 N N N 83 N O N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N N N 95 S C N 96 N C N 97 N O N 98 N C N 99 N C N 100 N C N 101 N O N 102 N O N 103 N O N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N N N 114 N C N 115 N C N 116 N O N 117 N O N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N N N 124 S C N 125 N C N 126 N O N 127 N C Y 128 N C Y 129 N N Y 130 N C Y 131 N C Y 132 N N N 133 N O 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 147 N N N 148 S C N 149 N C N 150 N O N 151 S C N 152 N C N 153 N C N 154 N C N 155 N O N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N N N 170 S C N 171 N C N 172 N O N 173 N C N 174 N C N 175 N C N 176 N C N 177 N O 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 H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N N N 192 S C N 193 N C N 194 N O N 195 N C N 196 N C N 197 N C N 198 N C N 199 N N N 200 N O N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H 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 N N 217 S C N 218 N C N 219 N O N 220 N C N 221 N C N 222 N S N 223 N C N 224 N O N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N N N 237 S C N 238 N C N 239 N O N 240 N C Y 241 N C Y 242 N C Y 243 N C Y 244 N C Y 245 N C Y 246 N C N 247 N O 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 N N 260 S C N 261 N C N 262 N O N 263 N C N 264 N C N 265 N C N 266 N O N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N N N 277 S C N 278 N C N 279 N O N 280 N C N 281 N O N 282 N O N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N N N 291 S C N 292 N C N 293 N O N 294 R C N 295 N O N 296 N C N 297 N O N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N H N 305 N H N 306 N H N 307 N N N 308 S C N 309 N C N 310 N O N 311 N C Y 312 N C Y 313 N C Y 314 N C Y 315 N C Y 316 N C Y 317 N C N 318 N O N 319 N O N 320 N H N 321 N H N 322 N H 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 N N 332 S C N 333 N C N 334 N O N 335 N C N 336 N C N 337 N C N 338 N O N 339 N H N 340 N H N 341 N H N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub 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 doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub 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 doub 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 sing N 69 N sing N 70 N sing N 71 N sing 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 doub 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 doub N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub N 114 N sing N 115 N sing 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 doub N 123 N sing N 124 N sing N 125 N sing N 126 N sing Y 127 N sing Y 128 N doub Y 129 N doub N 130 N sing Y 131 N sing N 132 N sing Y 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing 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 N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing 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 doub 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 sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing 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 sing 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 doub N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N doub N 231 N sing N 232 N sing N 233 N sing N 234 N sing Y 235 N doub Y 236 N sing Y 237 N sing N 238 N sing Y 239 N doub N 240 N sing Y 241 N doub N 242 N sing Y 243 N sing N 244 N sing N 245 N sing 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 doub 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 sing 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 sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N doub N 284 N sing N 285 N sing N 286 N sing N 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 doub N 300 N sing N 301 N sing N 302 N sing N 303 N sing Y 304 N doub Y 305 N sing Y 306 N sing N 307 N sing Y 308 N doub N 309 N sing Y 310 N doub N 311 N sing Y 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N doub N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing To Be Published 0353 An Artificial Intelligence Model for Translating Natural Language into Functional de Novo Proteins 10.2210/pdb9xzp/pdb pdb_00009xzp 100 1 N PIXEL 2025-07-19 DECTRIS EIGER2 X CdTe 16M SINGLE WAVELENGTH M x-ray 1 0.8856 1.0 ID23-1 ESRF 0.8856 SYNCHROTRON ESRF BEAMLINE ID23-1 8031.154 De novo protein 2 man polymer 18.015 water 113 nat water no no SGMKIAVIGATGQVGREIAKLLAEKGHEVTAIASRSKNPEEVAKLGIEAVYVDGEVLDFKSVEEAVKNADVVISVAGG SGMKIAVIGATGQVGREIAKLLAEKGHEVTAIASRSKNPEEVAKLGIEAVYVDGEVLDFKSVEEAVKNADVVISVAGG A,B polypeptide(L) 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 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 n n n n n n n n n n n n n n sample 1 78 32630 synthetic construct 562 Escherichia coli Biological sequence 1 2.28 46.01 VAPOR DIFFUSION, SITTING DROP 8.5 Morpheus G9: 30.0% w/v 550M_20K; 0.1 M MB3 pH 8.5; 0.1 M MCA 277 repository Initial release 1 0 2025-10-22 Not funded kat.wei@gmail.com 0000-0002-8794-1385 Kathy Wei Y principal investigator/group leader N RCSB Y RCSB 2025-08-27 REL REL HOH water N AlphaFold in silico model HOH 111 2 HOH HOH 101 A HOH 38 2 HOH HOH 102 A HOH 13 2 HOH HOH 103 A HOH 70 2 HOH HOH 104 A HOH 88 2 HOH HOH 105 A HOH 68 2 HOH HOH 106 A HOH 53 2 HOH HOH 107 A HOH 107 2 HOH HOH 108 A HOH 50 2 HOH HOH 109 A HOH 5 2 HOH HOH 110 A HOH 24 2 HOH HOH 111 A HOH 55 2 HOH HOH 112 A HOH 54 2 HOH HOH 113 A HOH 2 2 HOH HOH 114 A HOH 56 2 HOH HOH 115 A HOH 74 2 HOH HOH 116 A HOH 108 2 HOH HOH 117 A HOH 97 2 HOH HOH 118 A HOH 57 2 HOH HOH 119 A HOH 73 2 HOH HOH 120 A HOH 7 2 HOH HOH 121 A HOH 91 2 HOH HOH 122 A HOH 52 2 HOH HOH 123 A HOH 15 2 HOH HOH 124 A HOH 46 2 HOH HOH 125 A HOH 10 2 HOH HOH 126 A HOH 67 2 HOH HOH 127 A HOH 4 2 HOH HOH 128 A HOH 90 2 HOH HOH 129 A HOH 20 2 HOH HOH 130 A HOH 112 2 HOH HOH 131 A HOH 40 2 HOH HOH 132 A HOH 69 2 HOH HOH 133 A HOH 48 2 HOH HOH 134 A HOH 61 2 HOH HOH 135 A HOH 94 2 HOH HOH 136 A HOH 109 2 HOH HOH 137 A HOH 59 2 HOH HOH 138 A HOH 1 2 HOH HOH 139 A HOH 75 2 HOH HOH 140 A HOH 18 2 HOH HOH 141 A HOH 77 2 HOH HOH 142 A HOH 30 2 HOH HOH 143 A HOH 11 2 HOH HOH 144 A HOH 17 2 HOH HOH 145 A HOH 31 2 HOH HOH 146 A HOH 51 2 HOH HOH 147 A HOH 93 2 HOH HOH 148 A HOH 98 2 HOH HOH 149 A HOH 45 2 HOH HOH 150 A HOH 92 2 HOH HOH 151 A HOH 23 2 HOH HOH 152 A HOH 71 2 HOH HOH 153 A HOH 105 2 HOH HOH 154 A HOH 22 2 HOH HOH 155 A HOH 60 2 HOH HOH 156 A HOH 78 2 HOH HOH 101 B HOH 28 2 HOH HOH 102 B HOH 113 2 HOH HOH 103 B HOH 12 2 HOH HOH 104 B HOH 32 2 HOH HOH 105 B HOH 26 2 HOH HOH 106 B HOH 8 2 HOH HOH 107 B HOH 58 2 HOH HOH 108 B HOH 37 2 HOH HOH 109 B HOH 62 2 HOH HOH 110 B HOH 87 2 HOH HOH 111 B HOH 47 2 HOH HOH 112 B HOH 95 2 HOH HOH 113 B HOH 43 2 HOH HOH 114 B HOH 76 2 HOH HOH 115 B HOH 9 2 HOH HOH 116 B HOH 42 2 HOH HOH 117 B HOH 103 2 HOH HOH 118 B HOH 21 2 HOH HOH 119 B HOH 104 2 HOH HOH 120 B HOH 6 2 HOH HOH 121 B HOH 79 2 HOH HOH 122 B HOH 110 2 HOH HOH 123 B HOH 81 2 HOH HOH 124 B HOH 3 2 HOH HOH 125 B HOH 86 2 HOH HOH 126 B HOH 39 2 HOH HOH 127 B HOH 65 2 HOH HOH 128 B HOH 72 2 HOH HOH 129 B HOH 29 2 HOH HOH 130 B HOH 82 2 HOH HOH 131 B HOH 44 2 HOH HOH 132 B HOH 100 2 HOH HOH 133 B HOH 99 2 HOH HOH 134 B HOH 85 2 HOH HOH 135 B HOH 83 2 HOH HOH 136 B HOH 96 2 HOH HOH 137 B HOH 27 2 HOH HOH 138 B HOH 106 2 HOH HOH 139 B HOH 101 2 HOH HOH 140 B HOH 63 2 HOH HOH 141 B HOH 19 2 HOH HOH 142 B HOH 16 2 HOH HOH 143 B HOH 36 2 HOH HOH 144 B HOH 41 2 HOH HOH 145 B HOH 25 2 HOH HOH 146 B HOH 64 2 HOH HOH 147 B HOH 14 2 HOH HOH 148 B HOH 66 2 HOH HOH 149 B HOH 102 2 HOH HOH 150 B HOH 89 2 HOH HOH 151 B HOH 84 2 HOH HOH 152 B HOH 34 2 HOH HOH 153 B HOH 49 2 HOH HOH 154 B HOH 33 2 HOH HOH 155 B HOH 35 2 HOH HOH 156 B HOH 80 2 HOH HOH 157 B n 1 2 A GLY 3 n 2 GLY 3 A MET 4 n 3 MET 4 A LYS 5 n 4 LYS 5 A ILE 6 n 5 ILE 6 A ALA 7 n 6 ALA 7 A VAL 8 n 7 VAL 8 A ILE 9 n 8 ILE 9 A GLY 10 n 9 GLY 10 A ALA 11 n 10 ALA 11 A THR 12 n 11 THR 12 A GLY 13 n 12 GLY 13 A GLN 14 n 13 GLN 14 A VAL 15 n 14 VAL 15 A GLY 16 n 15 GLY 16 A ARG 17 n 16 ARG 17 A GLU 18 n 17 GLU 18 A ILE 19 n 18 ILE 19 A ALA 20 n 19 ALA 20 A LYS 21 n 20 LYS 21 A LEU 22 n 21 LEU 22 A LEU 23 n 22 LEU 23 A ALA 24 n 23 ALA 24 A GLU 25 n 24 GLU 25 A LYS 26 n 25 LYS 26 A GLY 27 n 26 GLY 27 A HIS 28 n 27 HIS 28 A GLU 29 n 28 GLU 29 A VAL 30 n 29 VAL 30 A THR 31 n 30 THR 31 A ALA 32 n 31 ALA 32 A ILE 33 n 32 ILE 33 A ALA 34 n 33 ALA 34 A SER 35 n 34 SER 35 A ARG 36 n 35 ARG 36 A SER 37 n 36 SER 37 A LYS 38 n 37 LYS 38 A ASN 39 n 38 ASN 39 A PRO 40 n 39 PRO 40 A GLU 41 n 40 GLU 41 A GLU 42 n 41 GLU 42 A VAL 43 n 42 VAL 43 A ALA 44 n 43 ALA 44 A LYS 45 n 44 LYS 45 A LEU 46 n 45 LEU 46 A GLY 47 n 46 GLY 47 A ILE 48 n 47 ILE 48 A GLU 49 n 48 GLU 49 A ALA 50 n 49 ALA 50 A VAL 51 n 50 VAL 51 A TYR 52 n 51 TYR 52 A VAL 53 n 52 VAL 53 A ASP 54 n 53 ASP 54 A GLY 55 n 54 GLY 55 A GLU 56 n 55 GLU 56 A VAL 57 n 56 VAL 57 A LEU 58 n 57 LEU 58 A ASP 59 n 58 ASP 59 A PHE 60 n 59 PHE 60 A LYS 61 n 60 LYS 61 A SER 62 n 61 SER 62 A VAL 63 n 62 VAL 63 A GLU 64 n 63 GLU 64 A GLU 65 n 64 GLU 65 A ALA 66 n 65 ALA 66 A VAL 67 n 66 VAL 67 A LYS 68 n 67 LYS 68 A ASN 69 n 68 ASN 69 A ALA 70 n 69 ALA 70 A ASP 71 n 70 ASP 71 A VAL 72 n 71 VAL 72 A VAL 73 n 72 VAL 73 A ILE 74 n 73 ILE 74 A SER 75 n 74 SER 75 A VAL 76 n 75 VAL 76 A ALA 77 n 76 ALA 77 A GLY 78 n 77 GLY 78 A GLY 79 n 78 GLY 79 A SER 2 n 1 SER 2 B GLY 3 n 2 GLY 3 B MET 4 n 3 MET 4 B LYS 5 n 4 LYS 5 B ILE 6 n 5 ILE 6 B ALA 7 n 6 ALA 7 B VAL 8 n 7 VAL 8 B ILE 9 n 8 ILE 9 B GLY 10 n 9 GLY 10 B ALA 11 n 10 ALA 11 B THR 12 n 11 THR 12 B GLY 13 n 12 GLY 13 B GLN 14 n 13 GLN 14 B VAL 15 n 14 VAL 15 B GLY 16 n 15 GLY 16 B ARG 17 n 16 ARG 17 B GLU 18 n 17 GLU 18 B ILE 19 n 18 ILE 19 B ALA 20 n 19 ALA 20 B LYS 21 n 20 LYS 21 B LEU 22 n 21 LEU 22 B LEU 23 n 22 LEU 23 B ALA 24 n 23 ALA 24 B GLU 25 n 24 GLU 25 B LYS 26 n 25 LYS 26 B GLY 27 n 26 GLY 27 B HIS 28 n 27 HIS 28 B GLU 29 n 28 GLU 29 B VAL 30 n 29 VAL 30 B THR 31 n 30 THR 31 B ALA 32 n 31 ALA 32 B ILE 33 n 32 ILE 33 B ALA 34 n 33 ALA 34 B SER 35 n 34 SER 35 B ARG 36 n 35 ARG 36 B SER 37 n 36 SER 37 B LYS 38 n 37 LYS 38 B ASN 39 n 38 ASN 39 B PRO 40 n 39 PRO 40 B GLU 41 n 40 GLU 41 B GLU 42 n 41 GLU 42 B VAL 43 n 42 VAL 43 B ALA 44 n 43 ALA 44 B LYS 45 n 44 LYS 45 B LEU 46 n 45 LEU 46 B GLY 47 n 46 GLY 47 B ILE 48 n 47 ILE 48 B GLU 49 n 48 GLU 49 B ALA 50 n 49 ALA 50 B VAL 51 n 50 VAL 51 B TYR 52 n 51 TYR 52 B VAL 53 n 52 VAL 53 B ASP 54 n 53 ASP 54 B GLY 55 n 54 GLY 55 B GLU 56 n 55 GLU 56 B VAL 57 n 56 VAL 57 B LEU 58 n 57 LEU 58 B ASP 59 n 58 ASP 59 B PHE 60 n 59 PHE 60 B LYS 61 n 60 LYS 61 B SER 62 n 61 SER 62 B VAL 63 n 62 VAL 63 B GLU 64 n 63 GLU 64 B GLU 65 n 64 GLU 65 B ALA 66 n 65 ALA 66 B VAL 67 n 66 VAL 67 B LYS 68 n 67 LYS 68 B ASN 69 n 68 ASN 69 B ALA 70 n 69 ALA 70 B ASP 71 n 70 ASP 71 B VAL 72 n 71 VAL 72 B VAL 73 n 72 VAL 73 B ILE 74 n 73 ILE 74 B SER 75 n 74 SER 75 B VAL 76 n 75 VAL 76 B ALA 77 n 76 ALA 77 B GLY 78 n 77 GLY 78 B GLY 79 n 78 GLY 79 B author_and_software_defined_assembly PISA 2 dimeric none 4610 -34 8340 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 A O GLU 29 A O GLU 28 A N ILE 6 A N ILE 5 A N ALA 7 A N ALA 6 B O ILE 74 B O ILE 73 B O VAL 73 B O VAL 72 A N ALA 77 A N ALA 76 A N ILE 74 A N ILE 73 B O ALA 7 B O ALA 6 B N ILE 6 B N ILE 5 B O THR 31 B O THR 30 A N GLU 49 A N GLU 48 B O ARG 36 B O ARG 35 1 A NZ LYS 5 A NZ LYS 4 0 Y 1 A CD GLN 14 A CD GLN 13 0 Y 1 A OE1 GLN 14 A OE1 GLN 13 0 Y 1 A NE2 GLN 14 A NE2 GLN 13 0 Y 1 A NZ LYS 38 A NZ LYS 37 0 Y 1 A CD GLU 49 B A CD GLU 48 0 Y 1 A OE1 GLU 49 B A OE1 GLU 48 0 Y 1 A OE2 GLU 49 B A OE2 GLU 48 0 Y 1 B NZ LYS 5 B NZ LYS 4 0 Y 1 B NZ LYS 21 B NZ LYS 20 0 Y 1 B CD GLU 29 B CD GLU 28 0 Y 1 B OE1 GLU 29 B OE1 GLU 28 0 Y 1 B OE2 GLU 29 B OE2 GLU 28 0 Y 1 B CE LYS 45 B CE LYS 44 0 Y 1 B NZ LYS 45 B NZ LYS 44 0 Y 1 B CD1 ILE 48 B CD1 ILE 47 0 Y 1 B CD GLU 49 B CD GLU 48 0 Y 1 B OE1 GLU 49 B OE1 GLU 48 0 Y 1 B OE2 GLU 49 B OE2 GLU 48 0 Y 1 B CE LYS 61 B CE LYS 60 0 Y 1 B NZ LYS 61 B NZ LYS 60 0 Y 1 B CD LYS 68 B CD LYS 67 0 Y 1 B CE LYS 68 B CE LYS 67 0 Y 1 B NZ LYS 68 B NZ LYS 67 0 Y 1 A SER 2 A SER 1 1 Y 1 B ALA 11 -86.52 44.34 1 B VAL 57 -87.78 -70.23 37.010 -1.157 -0.000 1.944 -1.832 -0.000 1.031 0.967 0.945 Hydrogens have been added in their riding positions 0.2450 0.1894 0.192 1.773 36.155 700 13402 14102 4.964 99.915 3.861 0.117 1 FREE R-VALUE MOLECULAR REPLACEMENT 0.134 0.136 0.800 0.800 1.200 MASK BULK SOLVENT 1.773 36.155 113 1233 0 0 1120 0.005 0.012 1178 0.002 0.016 1201 1.355 1.803 1607 0.496 1.735 2750 6.194 5.000 172 0.565 1.000 5 11.372 10.000 208 16.356 10.000 42 0.058 0.200 199 0.005 0.020 1406 0.001 0.020 226 0.201 0.200 188 0.180 0.200 953 0.151 0.200 566 0.075 0.200 591 0.118 0.200 85 0.002 0.200 1 0.146 0.200 53 0.117 0.200 6 2.572 3.547 647 2.568 3.539 646 3.832 6.350 813 3.832 6.356 814 3.197 3.950 531 3.194 3.949 531 4.906 7.092 787 4.903 7.097 788 6.542 33.587 1247 6.490 33.001 1223 0.321 1.819 50 977 99.6120 0.381 0.314 1.869 49 971 99.7067 0.322 0.264 1.923 50 923 99.7949 0.303 0.231 1.982 58 914 99.8972 0.313 0.220 2.046 44 860 100.0000 0.242 0.207 2.118 48 848 99.8885 0.299 0.196 2.198 33 824 100.0000 0.207 0.185 2.287 51 778 100.0000 0.211 0.175 2.388 39 763 100.0000 0.221 0.182 2.504 41 733 100.0000 0.268 0.200 2.639 35 691 100.0000 0.321 0.190 2.798 20 666 100.0000 0.344 0.214 2.990 15 629 100.0000 0.308 0.194 3.228 45 565 100.0000 0.256 0.205 3.533 25 531 100.0000 0.222 0.161 3.945 30 470 100.0000 0.202 0.139 4.547 29 429 100.0000 0.158 0.157 5.547 18 366 100.0000 0.190 0.174 7.754 13 289 100.0000 0.176 0.162 36.155 7 175 100.0000 1.773 36.155 Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary! 9XZP 14102 0.997 -0.408 0.0987 0.0399 0.1066 0.700 1 9.46 97645 99.7 6.92 3.55 99.9 0.0826 4.809 36.155 21.23 4985 4985 739 739 0.994 -0.593 0.0331 0.0891 0.512 99.8 6.75 3.64 100.0 0.0665 3.818 4.809 20.00 4588 4588 711 711 0.997 -0.230 0.0278 0.0722 0.538 99.8 6.45 3.35 100.0 0.0711 3.336 3.818 20.30 5116 5116 720 720 0.995 -0.393 0.0283 0.0766 0.537 100.0 7.11 3.67 100.0 0.0773 3.031 3.336 18.00 5120 5120 709 709 0.997 -0.337 0.0306 0.0832 0.602 100.0 7.22 3.72 100.0 0.0912 2.814 3.031 16.12 5145 5145 703 703 0.994 -0.331 0.0359 0.0981 0.619 100.0 7.32 3.77 100.0 0.0989 2.648 2.814 14.06 5008 5008 700 700 0.994 -0.107 0.0394 0.1066 0.682 100.0 7.15 3.67 100.0 0.1172 2.516 2.648 11.21 4458 4458 690 690 0.991 -0.223 0.0489 0.1272 0.695 99.5 6.46 3.34 100.0 0.1356 2.406 2.516 10.31 4627 4627 719 719 0.990 -0.093 0.0572 0.1475 0.711 99.3 6.44 3.31 100.0 0.1433 2.313 2.406 9.38 4775 4775 706 706 0.993 -0.046 0.0587 0.1550 0.767 99.9 6.76 3.46 100.0 0.1600 2.234 2.313 8.82 4748 4748 684 684 0.990 -0.097 0.0653 0.1730 0.769 99.8 6.94 3.52 100.0 0.1895 2.164 2.234 7.44 4973 4973 714 714 0.986 0.016 0.0770 0.2048 0.763 99.9 6.96 3.56 100.0 0.2342 2.102 2.164 6.54 4934 4934 703 703 0.983 0.003 0.0945 0.2528 0.806 100.0 7.02 3.58 100.0 0.2986 2.047 2.102 5.29 5021 5021 705 705 0.975 0.000 0.1192 0.3218 0.751 99.9 7.12 3.62 99.9 0.3525 1.997 2.047 4.58 5039 5039 700 700 0.960 0.001 0.1407 0.3799 0.796 100.0 7.20 3.67 100.0 0.4178 1.951 1.997 3.99 5006 5006 700 700 0.949 -0.040 0.1667 0.4503 0.763 99.7 7.15 3.65 99.9 0.5792 1.910 1.951 3.01 5044 5044 694 694 0.914 0.006 0.2290 0.6233 0.755 99.9 7.27 3.69 100.0 0.6776 1.872 1.910 2.49 4972 4972 700 700 0.864 -0.039 0.2707 0.7304 0.716 99.3 7.10 3.64 99.7 0.8007 1.836 1.872 2.08 4804 4804 695 695 0.825 0.001 0.3265 0.8659 0.742 99.4 6.91 3.53 99.7 0.9793 1.803 1.836 1.64 4660 4660 697 697 0.790 0.026 0.4064 1.0620 0.703 99.4 6.69 3.40 99.9 1.1616 1.773 1.803 1.43 4622 4622 713 713 0.688 0.081 0.4907 1.2633 0.758 99.3 6.48 3.30 99.6 data processing autoPROC 1.1.7 data scaling Aimless 0.8.2 data processing TRUNCATE 9.0.010 refinement REFMAC 5.8.0430 (refmacat 0.4.105) data reduction XDS phasing PHASER N Crystal structure of AI-designed homodimer MIYEI 1 N N 1 N N 2 N N 2 N N A GLY 13 A GLY 12 HELX_P A LYS 26 A LYS 25 1 AA1 14 A ASN 39 A ASN 38 HELX_P A LYS 45 A LYS 44 1 AA2 7 A ASP 59 A ASP 58 HELX_P A ASN 69 A ASN 68 1 AA3 11 B GLY 13 B GLY 12 HELX_P B LYS 26 B LYS 25 1 AA4 14 B ASN 39 B ASN 38 HELX_P B VAL 43 B VAL 42 5 AA5 5 B ASP 59 B ASP 58 HELX_P B ASN 69 B ASN 68 1 AA6 11 DE NOVO PROTEIN De novo protein MIYEI, DE NOVO PROTEIN 9XZP PDB 1 1 9XZP 2 79 9XZP 2 79 9XZP A 1 1 78 2 79 9XZP 2 79 9XZP B 1 1 78 6 2 parallel parallel anti-parallel parallel parallel anti-parallel A GLU 29 A GLU 28 A ALA 34 A ALA 33 A LYS 5 A LYS 4 A GLY 10 A GLY 9 B VAL 72 B VAL 71 B ALA 77 B ALA 76 A VAL 72 A VAL 71 A GLY 78 A GLY 77 B LYS 5 B LYS 4 B ILE 9 B ILE 8 B GLU 29 B GLU 28 B ALA 32 B ALA 31 A ILE 48 A ILE 47 A GLU 49 A GLU 48 B ARG 36 B ARG 35 B SER 37 B SER 36 5 C 1 2 1