0.007582 0.000000 0.000000 0.000000 0.007491 0.000000 0.000000 0.000000 0.022272 0.00000 0.00000 0.00000 Tu, C. Bard, J. Mosyak, L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 131.900 133.500 44.900 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 Cl -1 35.453 CHLORIDE ION non-polymer C3 H7 N O2 S 121.158 y CYSTEINE 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 C11 H12 N2 O2 204.225 y TRYPTOPHAN 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 To Be Published 0353 Optimization of a scFv-based biotherapeutic by CDR side-chain clash repair 80 1 PIXEL 2013-08-02 DECTRIS PILATUS 6M SINGLE WAVELENGTH M x-ray 1 1.0 1.0 17-ID APS 1.0 SYNCHROTRON APS BEAMLINE 17-ID 26559.936 scFv 3B4 1 man polymer 35.453 CHLORIDE ION 3 syn non-polymer 18.015 water 358 nat water no no QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAY MELSSLRSEDTAVYYCAREPDYYDSSGYYPIDAFDIWGQGTTVTVSSGGGGSGGGGSGGGGSQSALTQPASVSASPGQSI TISCTGTSSDVGAYDWVSWYQQHPGKAPKLLIFDVNNRPSGVSHRFSGSKSGNTASLTISGLQAEDEADYYCSSYTRRDT YVFGTGTKVTVLGE QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAY MELSSLRSEDTAVYYCAREPDYYDSSGYYPIDAFDIWGQGTTVTVSSGGGGSGGGGSGGGGSQSALTQPASVSASPGQSI TISCTGTSSDVGAYDWVSWYQQHPGKAPKLLIFDVNNRPSGVSHRFSGSKSGNTASLTISGLQAEDEADYYCSSYTRRDT YVFGTGTKVTVLGE H 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 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 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 n n n n n n n n n n n n n n n n n n n n Human sample 1 98 HEK293 IGHV1-69D 9606 Homo sapiens HEK293F 9606 Homo sapiens Biological sequence Human sample 99 142 HEK293 9606 Homo sapiens HEK293F 9606 Homo sapiens Biological sequence Human sample 143 234 HEK293 9606 Homo sapiens HEK293F 9606 Homo sapiens Biological sequence Human sample 235 254 HEK293 IGHV1-69-2 9606 Homo sapiens HEK293F 9606 Homo sapiens Biological sequence 3.6 66 very nice brick like VAPOR DIFFUSION, SITTING DROP 7.5 The concentration of 3B4 was 11 mg/ml in 20 mM Tris, pH 7.5 and 150 mM NaCl. Each drop contained 0.15 ul 3B4 and 0.15 ul reservoir solution containing 100 mM HEPES, pH 7.5 and 4300 mM NaCl. 291 pdbx_struct_assembly_auth_evidence pdbx_struct_oper_list atom_site atom_site_anisotrop entity entity_poly entity_poly_seq entity_src_gen pdbx_distant_solvent_atoms pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_poly_seq_scheme pdbx_struct_assembly pdbx_struct_assembly_gen pdbx_struct_assembly_prop pdbx_struct_sheet_hbond pdbx_struct_special_symmetry pdbx_unobs_or_zero_occ_residues pdbx_validate_torsion struct struct_asym struct_biol struct_conf struct_conn struct_ref struct_ref_seq struct_ref_seq_dif struct_sheet_range struct_site struct_site_gen atom_site pdbx_distant_solvent_atoms pdbx_nonpoly_scheme pdbx_struct_special_symmetry struct_site struct_site_gen repository Initial release Author supporting evidence Derived calculations Advisory Atomic model Data collection Database references Derived calculations Polymer sequence Source and taxonomy Structure summary Advisory Atomic model Data collection Derived calculations 1 0 2015-11-04 1 1 2017-11-01 2 0 2019-12-25 3 0 2020-06-17 _pdbx_struct_oper_list.symmetry_operation _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_seq_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.occupancy _atom_site_anisotrop.pdbx_auth_asym_id _atom_site_anisotrop.pdbx_auth_seq_id _atom_site_anisotrop.pdbx_label_asym_id _atom_site_anisotrop.pdbx_label_seq_id _entity_poly_seq.entity_id _entity_poly_seq.num _entity_src_gen.entity_id _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.pdbx_src_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_entity_nonpoly.entity_id _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.seq_id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_prop.value _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.label_asym_id _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_seq_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _struct.pdbx_descriptor _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_seq_id _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end _struct_ref_seq.pdbx_db_accession _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.seq_align_end _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_site.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_seq_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_comp_id _struct_site_gen.auth_seq_id _struct_site_gen.label_asym_id _struct_site_gen.label_comp_id _struct_site_gen.label_seq_id _atom_site.auth_seq_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_struct_special_symmetry.auth_seq_id _struct_site.details _struct_site.pdbx_auth_seq_id _struct_site_gen.auth_seq_id N RCSB Y RCSB 2015-06-15 REL REL 1 H O HOH 1657 5.91 1 H O HOH 1658 6.36 CL CHLORIDE ION HOH water CL 3 2 CL CL 1201 H CL 1 2 CL CL 1202 H CL 2 2 CL CL 1203 H HOH 214 3 HOH HOH 1301 H HOH 163 3 HOH HOH 1302 H HOH 142 3 HOH HOH 1303 H HOH 241 3 HOH HOH 1304 H HOH 354 3 HOH HOH 1305 H HOH 85 3 HOH HOH 1306 H HOH 319 3 HOH HOH 1307 H HOH 47 3 HOH HOH 1308 H HOH 336 3 HOH HOH 1309 H HOH 149 3 HOH HOH 1310 H HOH 191 3 HOH HOH 1311 H HOH 150 3 HOH HOH 1312 H HOH 89 3 HOH HOH 1313 H HOH 272 3 HOH HOH 1314 H HOH 30 3 HOH HOH 1315 H HOH 170 3 HOH HOH 1316 H HOH 300 3 HOH HOH 1317 H HOH 33 3 HOH HOH 1318 H HOH 95 3 HOH HOH 1319 H HOH 104 3 HOH HOH 1320 H HOH 166 3 HOH HOH 1321 H HOH 153 3 HOH HOH 1322 H HOH 296 3 HOH HOH 1323 H HOH 183 3 HOH HOH 1324 H HOH 124 3 HOH HOH 1325 H HOH 87 3 HOH HOH 1326 H HOH 159 3 HOH HOH 1327 H HOH 232 3 HOH HOH 1328 H HOH 125 3 HOH HOH 1329 H HOH 71 3 HOH HOH 1330 H HOH 122 3 HOH HOH 1331 H HOH 324 3 HOH HOH 1332 H HOH 206 3 HOH HOH 1333 H HOH 59 3 HOH HOH 1334 H HOH 282 3 HOH HOH 1335 H HOH 21 3 HOH HOH 1336 H HOH 34 3 HOH HOH 1337 H HOH 75 3 HOH HOH 1338 H HOH 281 3 HOH HOH 1339 H HOH 134 3 HOH HOH 1340 H HOH 148 3 HOH HOH 1341 H HOH 182 3 HOH HOH 1342 H HOH 229 3 HOH HOH 1343 H HOH 139 3 HOH HOH 1344 H HOH 193 3 HOH HOH 1345 H HOH 132 3 HOH HOH 1346 H HOH 19 3 HOH HOH 1347 H HOH 189 3 HOH HOH 1348 H HOH 176 3 HOH HOH 1349 H HOH 128 3 HOH HOH 1350 H HOH 49 3 HOH HOH 1351 H HOH 247 3 HOH HOH 1352 H HOH 42 3 HOH HOH 1353 H HOH 294 3 HOH HOH 1354 H HOH 307 3 HOH HOH 1355 H HOH 44 3 HOH HOH 1356 H HOH 81 3 HOH HOH 1357 H HOH 79 3 HOH HOH 1358 H HOH 43 3 HOH HOH 1359 H HOH 88 3 HOH HOH 1360 H HOH 94 3 HOH HOH 1361 H HOH 352 3 HOH HOH 1362 H HOH 52 3 HOH HOH 1363 H HOH 16 3 HOH HOH 1364 H HOH 83 3 HOH HOH 1365 H HOH 65 3 HOH HOH 1366 H HOH 287 3 HOH HOH 1367 H HOH 74 3 HOH HOH 1368 H HOH 199 3 HOH HOH 1369 H HOH 285 3 HOH HOH 1370 H HOH 129 3 HOH HOH 1371 H HOH 12 3 HOH HOH 1372 H HOH 51 3 HOH HOH 1373 H HOH 255 3 HOH HOH 1374 H HOH 20 3 HOH HOH 1375 H HOH 290 3 HOH HOH 1376 H HOH 179 3 HOH HOH 1377 H HOH 13 3 HOH HOH 1378 H HOH 119 3 HOH HOH 1379 H HOH 54 3 HOH HOH 1380 H HOH 292 3 HOH HOH 1381 H HOH 92 3 HOH HOH 1382 H HOH 263 3 HOH HOH 1383 H HOH 108 3 HOH HOH 1384 H HOH 257 3 HOH HOH 1385 H HOH 102 3 HOH HOH 1386 H HOH 113 3 HOH HOH 1387 H HOH 40 3 HOH HOH 1388 H HOH 63 3 HOH HOH 1389 H HOH 80 3 HOH HOH 1390 H HOH 10 3 HOH HOH 1391 H HOH 101 3 HOH HOH 1392 H HOH 218 3 HOH HOH 1393 H HOH 25 3 HOH HOH 1394 H HOH 18 3 HOH HOH 1395 H HOH 84 3 HOH HOH 1396 H HOH 143 3 HOH HOH 1397 H HOH 205 3 HOH HOH 1398 H HOH 98 3 HOH HOH 1399 H HOH 72 3 HOH HOH 1400 H HOH 306 3 HOH HOH 1401 H HOH 133 3 HOH HOH 1402 H HOH 26 3 HOH HOH 1403 H HOH 56 3 HOH HOH 1404 H HOH 250 3 HOH HOH 1405 H HOH 121 3 HOH HOH 1406 H HOH 53 3 HOH HOH 1407 H HOH 107 3 HOH HOH 1408 H HOH 225 3 HOH HOH 1409 H HOH 130 3 HOH HOH 1410 H HOH 197 3 HOH HOH 1411 H HOH 68 3 HOH HOH 1412 H HOH 105 3 HOH HOH 1413 H HOH 91 3 HOH HOH 1414 H HOH 190 3 HOH HOH 1415 H HOH 325 3 HOH HOH 1416 H HOH 62 3 HOH HOH 1417 H HOH 46 3 HOH HOH 1418 H HOH 27 3 HOH HOH 1419 H HOH 209 3 HOH HOH 1420 H HOH 112 3 HOH HOH 1421 H HOH 253 3 HOH HOH 1422 H HOH 28 3 HOH HOH 1423 H HOH 78 3 HOH HOH 1424 H HOH 37 3 HOH HOH 1425 H HOH 184 3 HOH HOH 1426 H HOH 308 3 HOH HOH 1427 H HOH 332 3 HOH HOH 1428 H HOH 135 3 HOH HOH 1429 H HOH 192 3 HOH HOH 1430 H HOH 66 3 HOH HOH 1431 H HOH 138 3 HOH HOH 1432 H HOH 58 3 HOH HOH 1433 H HOH 201 3 HOH HOH 1434 H HOH 29 3 HOH HOH 1435 H HOH 41 3 HOH HOH 1436 H HOH 293 3 HOH HOH 1437 H HOH 77 3 HOH HOH 1438 H HOH 155 3 HOH HOH 1439 H HOH 228 3 HOH HOH 1440 H HOH 164 3 HOH HOH 1441 H HOH 140 3 HOH HOH 1442 H HOH 69 3 HOH HOH 1443 H HOH 310 3 HOH HOH 1444 H HOH 357 3 HOH HOH 1445 H HOH 93 3 HOH HOH 1446 H HOH 57 3 HOH HOH 1447 H HOH 24 3 HOH HOH 1448 H HOH 70 3 HOH HOH 1449 H HOH 180 3 HOH HOH 1450 H HOH 323 3 HOH HOH 1451 H HOH 297 3 HOH HOH 1452 H HOH 169 3 HOH HOH 1453 H HOH 118 3 HOH HOH 1454 H HOH 67 3 HOH HOH 1455 H HOH 15 3 HOH HOH 1456 H HOH 73 3 HOH HOH 1457 H HOH 156 3 HOH HOH 1458 H HOH 167 3 HOH HOH 1459 H HOH 36 3 HOH HOH 1460 H HOH 329 3 HOH HOH 1461 H HOH 295 3 HOH HOH 1462 H HOH 11 3 HOH HOH 1463 H HOH 266 3 HOH HOH 1464 H HOH 196 3 HOH HOH 1465 H HOH 326 3 HOH HOH 1466 H HOH 265 3 HOH HOH 1467 H HOH 252 3 HOH HOH 1468 H HOH 322 3 HOH HOH 1469 H HOH 312 3 HOH HOH 1470 H HOH 7 3 HOH HOH 1471 H HOH 286 3 HOH HOH 1472 H HOH 279 3 HOH HOH 1473 H HOH 299 3 HOH HOH 1474 H HOH 284 3 HOH HOH 1475 H HOH 50 3 HOH HOH 1476 H HOH 137 3 HOH HOH 1477 H HOH 235 3 HOH HOH 1478 H HOH 106 3 HOH HOH 1479 H HOH 254 3 HOH HOH 1480 H HOH 114 3 HOH HOH 1481 H HOH 353 3 HOH HOH 1482 H HOH 223 3 HOH HOH 1483 H HOH 351 3 HOH HOH 1484 H HOH 213 3 HOH HOH 1485 H HOH 131 3 HOH HOH 1486 H HOH 86 3 HOH HOH 1487 H HOH 31 3 HOH HOH 1488 H HOH 291 3 HOH HOH 1489 H HOH 177 3 HOH HOH 1490 H HOH 289 3 HOH HOH 1491 H HOH 39 3 HOH HOH 1492 H HOH 181 3 HOH HOH 1493 H HOH 55 3 HOH HOH 1494 H HOH 61 3 HOH HOH 1495 H HOH 267 3 HOH HOH 1496 H HOH 146 3 HOH HOH 1497 H HOH 283 3 HOH HOH 1498 H HOH 45 3 HOH HOH 1499 H HOH 288 3 HOH HOH 1500 H HOH 35 3 HOH HOH 1501 H HOH 6 3 HOH HOH 1502 H HOH 215 3 HOH HOH 1503 H HOH 103 3 HOH HOH 1504 H HOH 126 3 HOH HOH 1505 H HOH 202 3 HOH HOH 1506 H HOH 141 3 HOH HOH 1507 H HOH 123 3 HOH HOH 1508 H HOH 208 3 HOH HOH 1509 H HOH 328 3 HOH HOH 1510 H HOH 280 3 HOH HOH 1511 H HOH 302 3 HOH HOH 1512 H HOH 222 3 HOH HOH 1513 H HOH 48 3 HOH HOH 1514 H HOH 4 3 HOH HOH 1515 H HOH 174 3 HOH HOH 1516 H HOH 200 3 HOH HOH 1517 H HOH 260 3 HOH HOH 1518 H HOH 226 3 HOH HOH 1519 H HOH 144 3 HOH HOH 1520 H HOH 17 3 HOH HOH 1521 H HOH 210 3 HOH HOH 1522 H HOH 173 3 HOH HOH 1523 H HOH 162 3 HOH HOH 1524 H HOH 2 3 HOH HOH 1525 H HOH 203 3 HOH HOH 1526 H HOH 224 3 HOH HOH 1527 H HOH 256 3 HOH HOH 1528 H HOH 158 3 HOH HOH 1529 H HOH 154 3 HOH HOH 1530 H HOH 186 3 HOH HOH 1531 H HOH 327 3 HOH HOH 1532 H HOH 9 3 HOH HOH 1533 H HOH 110 3 HOH HOH 1534 H HOH 90 3 HOH HOH 1535 H HOH 100 3 HOH HOH 1536 H HOH 14 3 HOH HOH 1537 H HOH 38 3 HOH HOH 1538 H HOH 220 3 HOH HOH 1539 H HOH 8 3 HOH HOH 1540 H HOH 3 3 HOH HOH 1541 H HOH 301 3 HOH HOH 1542 H HOH 240 3 HOH HOH 1543 H HOH 32 3 HOH HOH 1544 H HOH 22 3 HOH HOH 1545 H HOH 345 3 HOH HOH 1546 H HOH 23 3 HOH HOH 1547 H HOH 204 3 HOH HOH 1548 H HOH 314 3 HOH HOH 1549 H HOH 330 3 HOH HOH 1550 H HOH 317 3 HOH HOH 1551 H HOH 60 3 HOH HOH 1552 H HOH 278 3 HOH HOH 1553 H HOH 318 3 HOH HOH 1554 H HOH 172 3 HOH HOH 1555 H HOH 161 3 HOH HOH 1556 H HOH 187 3 HOH HOH 1557 H HOH 5 3 HOH HOH 1558 H HOH 64 3 HOH HOH 1559 H HOH 175 3 HOH HOH 1560 H HOH 233 3 HOH HOH 1561 H HOH 234 3 HOH HOH 1562 H HOH 168 3 HOH HOH 1563 H HOH 303 3 HOH HOH 1564 H HOH 316 3 HOH HOH 1565 H HOH 298 3 HOH HOH 1566 H HOH 320 3 HOH HOH 1567 H HOH 304 3 HOH HOH 1568 H HOH 1 3 HOH HOH 1569 H HOH 251 3 HOH HOH 1570 H HOH 82 3 HOH HOH 1571 H HOH 237 3 HOH HOH 1572 H HOH 198 3 HOH HOH 1573 H HOH 309 3 HOH HOH 1574 H HOH 239 3 HOH HOH 1575 H HOH 152 3 HOH HOH 1576 H HOH 227 3 HOH HOH 1577 H HOH 269 3 HOH HOH 1578 H HOH 236 3 HOH HOH 1579 H HOH 277 3 HOH HOH 1580 H HOH 231 3 HOH HOH 1581 H HOH 96 3 HOH HOH 1582 H HOH 262 3 HOH HOH 1583 H HOH 248 3 HOH HOH 1584 H HOH 348 3 HOH HOH 1585 H HOH 264 3 HOH HOH 1586 H HOH 321 3 HOH HOH 1587 H HOH 338 3 HOH HOH 1588 H HOH 212 3 HOH HOH 1589 H HOH 111 3 HOH HOH 1590 H HOH 350 3 HOH HOH 1591 H HOH 127 3 HOH HOH 1592 H HOH 244 3 HOH HOH 1593 H HOH 115 3 HOH HOH 1594 H HOH 315 3 HOH HOH 1595 H HOH 271 3 HOH HOH 1596 H HOH 194 3 HOH HOH 1597 H HOH 97 3 HOH HOH 1598 H HOH 76 3 HOH HOH 1599 H HOH 243 3 HOH HOH 1600 H HOH 335 3 HOH HOH 1601 H HOH 333 3 HOH HOH 1602 H HOH 340 3 HOH HOH 1603 H HOH 258 3 HOH HOH 1604 H HOH 99 3 HOH HOH 1605 H HOH 221 3 HOH HOH 1606 H HOH 358 3 HOH HOH 1607 H HOH 178 3 HOH HOH 1608 H HOH 219 3 HOH HOH 1609 H HOH 331 3 HOH HOH 1610 H HOH 347 3 HOH HOH 1611 H HOH 151 3 HOH HOH 1612 H HOH 349 3 HOH HOH 1613 H HOH 160 3 HOH HOH 1614 H HOH 268 3 HOH HOH 1615 H HOH 120 3 HOH HOH 1616 H HOH 259 3 HOH HOH 1617 H HOH 342 3 HOH HOH 1618 H HOH 116 3 HOH HOH 1619 H HOH 242 3 HOH HOH 1620 H HOH 171 3 HOH HOH 1621 H HOH 157 3 HOH HOH 1622 H HOH 207 3 HOH HOH 1623 H HOH 185 3 HOH HOH 1624 H HOH 275 3 HOH HOH 1625 H HOH 334 3 HOH HOH 1626 H HOH 147 3 HOH HOH 1627 H HOH 145 3 HOH HOH 1628 H HOH 165 3 HOH HOH 1629 H HOH 343 3 HOH HOH 1630 H HOH 313 3 HOH HOH 1631 H HOH 355 3 HOH HOH 1632 H HOH 346 3 HOH HOH 1633 H HOH 188 3 HOH HOH 1634 H HOH 341 3 HOH HOH 1635 H HOH 305 3 HOH HOH 1636 H HOH 211 3 HOH HOH 1637 H HOH 230 3 HOH HOH 1638 H HOH 216 3 HOH HOH 1639 H HOH 261 3 HOH HOH 1640 H HOH 109 3 HOH HOH 1641 H HOH 276 3 HOH HOH 1642 H HOH 136 3 HOH HOH 1643 H HOH 311 3 HOH HOH 1644 H HOH 117 3 HOH HOH 1645 H HOH 195 3 HOH HOH 1646 H HOH 337 3 HOH HOH 1647 H HOH 274 3 HOH HOH 1648 H HOH 217 3 HOH HOH 1649 H HOH 249 3 HOH HOH 1650 H HOH 356 3 HOH HOH 1651 H HOH 238 3 HOH HOH 1652 H HOH 246 3 HOH HOH 1653 H HOH 344 3 HOH HOH 1654 H HOH 270 3 HOH HOH 1655 H HOH 273 3 HOH HOH 1656 H HOH 339 3 HOH HOH 1657 H HOH 245 3 HOH HOH 1658 H GLN 1 n 1 GLN 1 H VAL 2 n 2 VAL 2 H GLN 3 n 3 GLN 3 H LEU 4 n 4 LEU 4 H VAL 5 n 5 VAL 5 H GLN 6 n 6 GLN 6 H SER 7 n 7 SER 7 H GLY 8 n 8 GLY 8 H ALA 9 n 9 ALA 9 H GLU 10 n 10 GLU 10 H VAL 11 n 11 VAL 11 H LYS 12 n 12 LYS 12 H LYS 13 n 13 LYS 13 H PRO 14 n 14 PRO 14 H GLY 15 n 15 GLY 15 H SER 16 n 16 SER 16 H SER 17 n 17 SER 17 H VAL 18 n 18 VAL 18 H LYS 19 n 19 LYS 19 H VAL 20 n 20 VAL 20 H SER 21 n 21 SER 21 H CYS 22 n 22 CYS 22 H LYS 23 n 23 LYS 23 H ALA 24 n 24 ALA 24 H SER 25 n 25 SER 25 H GLY 26 n 26 GLY 26 H GLY 27 n 27 GLY 27 H THR 28 n 28 THR 28 H PHE 29 n 29 PHE 29 H SER 30 n 30 SER 30 H SER 31 n 31 SER 31 H TYR 32 n 32 TYR 32 H ALA 33 n 33 ALA 33 H ILE 34 n 34 ILE 34 H SER 35 n 35 SER 35 H TRP 36 n 36 TRP 36 H VAL 37 n 37 VAL 37 H ARG 38 n 38 ARG 38 H GLN 39 n 39 GLN 39 H ALA 40 n 40 ALA 40 H PRO 41 n 41 PRO 41 H GLY 42 n 42 GLY 42 H GLN 43 n 43 GLN 43 H GLY 44 n 44 GLY 44 H LEU 45 n 45 LEU 45 H GLU 46 n 46 GLU 46 H TRP 47 n 47 TRP 47 H MET 48 n 48 MET 48 H GLY 49 n 49 GLY 49 H GLY 50 n 50 GLY 50 H ILE 51 n 51 ILE 51 H ILE 52 n 52 ILE 52 H PRO 53 n 53 PRO 53 H ILE 54 n 54 ILE 54 H PHE 55 n 55 PHE 55 H GLY 56 n 56 GLY 56 H THR 57 n 57 THR 57 H ALA 58 n 58 ALA 58 H ASN 59 n 59 ASN 59 H TYR 60 n 60 TYR 60 H ALA 61 n 61 ALA 61 H GLN 62 n 62 GLN 62 H LYS 63 n 63 LYS 63 H PHE 64 n 64 PHE 64 H GLN 65 n 65 GLN 65 H GLY 66 n 66 GLY 66 H ARG 67 n 67 ARG 67 H VAL 68 n 68 VAL 68 H THR 69 n 69 THR 69 H ILE 70 n 70 ILE 70 H THR 71 n 71 THR 71 H ALA 72 n 72 ALA 72 H ASP 73 n 73 ASP 73 H GLU 74 n 74 GLU 74 H SER 75 n 75 SER 75 H THR 76 n 76 THR 76 H SER 77 n 77 SER 77 H THR 78 n 78 THR 78 H ALA 79 n 79 ALA 79 H TYR 80 n 80 TYR 80 H MET 81 n 81 MET 81 H GLU 82 n 82 GLU 82 H LEU 83 n 83 LEU 83 H SER 84 n 84 SER 84 H SER 85 n 85 SER 85 H LEU 86 n 86 LEU 86 H ARG 87 n 87 ARG 87 H SER 88 n 88 SER 88 H GLU 89 n 89 GLU 89 H ASP 90 n 90 ASP 90 H THR 91 n 91 THR 91 H ALA 92 n 92 ALA 92 H VAL 93 n 93 VAL 93 H TYR 94 n 94 TYR 94 H TYR 95 n 95 TYR 95 H CYS 96 n 96 CYS 96 H ALA 97 n 97 ALA 97 H ARG 98 n 98 ARG 98 H GLU 99 n 99 GLU 99 H PRO 100 n 100 PRO 100 H ASP 101 n 101 ASP 101 H TYR 102 n 102 TYR 102 H TYR 103 n 103 TYR 103 H ASP 104 n 104 ASP 104 H SER 105 n 105 SER 105 H SER 106 n 106 SER 106 H GLY 107 n 107 GLY 107 H TYR 108 n 108 TYR 108 H TYR 109 n 109 TYR 109 H PRO 110 n 110 PRO 110 H ILE 111 n 111 ILE 111 H ASP 112 n 112 ASP 112 H ALA 113 n 113 ALA 113 H PHE 114 n 114 PHE 114 H ASP 115 n 115 ASP 115 H ILE 116 n 116 ILE 116 H TRP 117 n 117 TRP 117 H GLY 118 n 118 GLY 118 H GLN 119 n 119 GLN 119 H GLY 120 n 120 GLY 120 H THR 121 n 121 THR 121 H THR 122 n 122 THR 122 H VAL 123 n 123 VAL 123 H THR 124 n 124 THR 124 H VAL 125 n 125 VAL 125 H SER 126 n 126 SER 126 H SER 127 n 127 SER 127 H GLY 128 n 128 GLY 128 H GLY 129 n 129 GLY 129 H GLY 130 n 130 GLY 130 H n 131 131 H n 132 132 H n 133 133 H n 134 134 H n 135 135 H n 136 136 H n 137 137 H n 138 138 H n 139 139 H n 140 140 H n 141 141 H n 142 142 H n 143 1001 H SER 2 n 144 SER 1002 H ALA 3 n 145 ALA 1003 H LEU 4 n 146 LEU 1004 H THR 5 n 147 THR 1005 H GLN 6 n 148 GLN 1006 H PRO 7 n 149 PRO 1007 H ALA 8 n 150 ALA 1008 H SER 9 n 151 SER 1009 H VAL 10 n 152 VAL 1010 H SER 11 n 153 SER 1011 H ALA 12 n 154 ALA 1012 H SER 13 n 155 SER 1013 H PRO 14 n 156 PRO 1014 H GLY 15 n 157 GLY 1015 H GLN 16 n 158 GLN 1016 H SER 17 n 159 SER 1017 H ILE 18 n 160 ILE 1018 H THR 19 n 161 THR 1019 H ILE 20 n 162 ILE 1020 H SER 21 n 163 SER 1021 H CYS 22 n 164 CYS 1022 H THR 23 n 165 THR 1023 H GLY 24 n 166 GLY 1024 H THR 25 n 167 THR 1025 H SER 26 n 168 SER 1026 H SER 27 n 169 SER 1027 H ASP 28 n 170 ASP 1028 H VAL 29 n 171 VAL 1029 H GLY 30 n 172 GLY 1030 H ALA 31 n 173 ALA 1031 H TYR 32 n 174 TYR 1032 H ASP 33 n 175 ASP 1033 H TRP 34 n 176 TRP 1034 H VAL 35 n 177 VAL 1035 H SER 36 n 178 SER 1036 H TRP 37 n 179 TRP 1037 H TYR 38 n 180 TYR 1038 H GLN 39 n 181 GLN 1039 H GLN 40 n 182 GLN 1040 H HIS 41 n 183 HIS 1041 H PRO 42 n 184 PRO 1042 H GLY 43 n 185 GLY 1043 H LYS 44 n 186 LYS 1044 H ALA 45 n 187 ALA 1045 H PRO 46 n 188 PRO 1046 H LYS 47 n 189 LYS 1047 H LEU 48 n 190 LEU 1048 H LEU 49 n 191 LEU 1049 H ILE 50 n 192 ILE 1050 H PHE 51 n 193 PHE 1051 H ASP 52 n 194 ASP 1052 H VAL 53 n 195 VAL 1053 H ASN 54 n 196 ASN 1054 H ASN 55 n 197 ASN 1055 H ARG 56 n 198 ARG 1056 H PRO 57 n 199 PRO 1057 H SER 58 n 200 SER 1058 H GLY 59 n 201 GLY 1059 H VAL 60 n 202 VAL 1060 H SER 61 n 203 SER 1061 H HIS 62 n 204 HIS 1062 H ARG 63 n 205 ARG 1063 H PHE 64 n 206 PHE 1064 H SER 65 n 207 SER 1065 H GLY 66 n 208 GLY 1066 H SER 67 n 209 SER 1067 H LYS 68 n 210 LYS 1068 H SER 69 n 211 SER 1069 H GLY 70 n 212 GLY 1070 H ASN 71 n 213 ASN 1071 H THR 72 n 214 THR 1072 H ALA 73 n 215 ALA 1073 H SER 74 n 216 SER 1074 H LEU 75 n 217 LEU 1075 H THR 76 n 218 THR 1076 H ILE 77 n 219 ILE 1077 H SER 78 n 220 SER 1078 H GLY 79 n 221 GLY 1079 H LEU 80 n 222 LEU 1080 H GLN 81 n 223 GLN 1081 H ALA 82 n 224 ALA 1082 H GLU 83 n 225 GLU 1083 H ASP 84 n 226 ASP 1084 H GLU 85 n 227 GLU 1085 H ALA 86 n 228 ALA 1086 H ASP 87 n 229 ASP 1087 H TYR 88 n 230 TYR 1088 H TYR 89 n 231 TYR 1089 H CYS 90 n 232 CYS 1090 H SER 91 n 233 SER 1091 H SER 92 n 234 SER 1092 H TYR 93 n 235 TYR 1093 H THR 94 n 236 THR 1094 H ARG 95 n 237 ARG 1095 H ARG 96 n 238 ARG 1096 H ASP 97 n 239 ASP 1097 H THR 98 n 240 THR 1098 H TYR 99 n 241 TYR 1099 H VAL 100 n 242 VAL 1100 H PHE 101 n 243 PHE 1101 H GLY 102 n 244 GLY 1102 H THR 103 n 245 THR 1103 H GLY 104 n 246 GLY 1104 H THR 105 n 247 THR 1105 H LYS 106 n 248 LYS 1106 H VAL 107 n 249 VAL 1107 H THR 108 n 250 THR 1108 H VAL 109 n 251 VAL 1109 H LEU 110 n 252 LEU 1110 H GLY 111 n 253 GLY 1111 H GLU 112 n 254 GLU 1112 H 1.2805 -1.5347 -0.8531 4.0172 1.5531 1.6197 -0.0341 -0.0129 -0.1756 0.1706 -0.0706 0.2777 0.1808 -0.1303 0.1030 0.1578 0.0167 0.0117 0.1651 0.0019 0.1405 scFv heavy chain refined 34.8223 19.1209 11.8111 X-RAY DIFFRACTION 2.8645 0.1904 -0.4138 1.7781 -0.3412 1.2041 0.0628 0.0247 -0.0222 -0.0412 -0.0032 0.1022 -0.0232 0.0083 -0.0450 0.0921 0.0284 0.0122 0.0893 0.0072 0.1006 scFv light chain refined 55.1060 14.5684 9.3845 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 chain H X-RAY DIFFRACTION 2 chain L author_defined_assembly 1 monomeric gel filtration 390 -27 11300 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 H N VAL 5 A N VAL 5 H O LYS 23 A O LYS 23 H N VAL 20 A N VAL 20 H O MET 81 A O MET 81 H O THR 78 A O THR 78 H N ASP 73 A N ASP 73 H N GLU 10 A N GLU 10 H O THR 124 A O THR 124 H O THR 121 A O THR 121 H N TYR 94 A N TYR 94 H N TYR 102 A N TYR 102 H O TYR 109 A O TYR 109 H O ASN 59 A O ASN 59 H N GLY 50 A N GLY 50 H O MET 48 A O MET 48 H N TRP 36 A N TRP 36 H N VAL 37 A N VAL 37 H O TYR 95 A O TYR 95 H N ARG 98 A N ARG 98 H O ILE 116 A O ILE 116 H N VAL 1010 A N VAL 152 H O THR 1108 A O THR 250 H O VAL 1107 A O VAL 249 H N ALA 1086 A N ALA 228 H O ASP 1087 A O ASP 229 H N GLN 1040 A N GLN 182 H N TRP 1037 A N TRP 179 H O LEU 1049 A O LEU 191 H N VAL 1010 A N VAL 152 H O THR 1108 A O THR 250 H O VAL 1107 A O VAL 249 H N ALA 1086 A N ALA 228 H N SER 1092 A N SER 234 H O VAL 1100 A O VAL 242 H N ILE 1018 A N ILE 160 H O ILE 1077 A O ILE 219 H O THR 1076 A O THR 218 H N SER 1065 A N SER 207 1 H HOH 1320 E HOH 1 H HOH 1440 E HOH 1 H GLY 131 A GLY 131 1 Y 1 H SER 132 A SER 132 1 Y 1 H GLY 133 A GLY 133 1 Y 1 H GLY 134 A GLY 134 1 Y 1 H GLY 135 A GLY 135 1 Y 1 H GLY 136 A GLY 136 1 Y 1 H SER 137 A SER 137 1 Y 1 H GLY 138 A GLY 138 1 Y 1 H GLY 139 A GLY 139 1 Y 1 H GLY 140 A GLY 140 1 Y 1 H GLY 141 A GLY 141 1 Y 1 H SER 142 A SER 142 1 Y 1 H GLN 1001 A GLN 143 1 Y 1 H ASP 104 -141.71 -158.15 1 H ASP 1028 -128.39 -94.56 1 H VAL 1053 71.56 -48.02 0.1944 0.1791 0.1798 1.4049 32.975 3850 77314 4.98 99.68 0.14 Random selection 1 THROUGHOUT 1.34 MOLECULAR REPLACEMENT 19.93 0.90 1.11 E10 ML FLAT BULK SOLVENT MODEL 1.4049 32.975 358 2167 3 0 1806 0.006 1976 1.067 2716 11.698 729 0.079 299 0.004 352 0.2866 0.2646 1.4221 135 2475 96.00 0.2748 0.2430 1.4401 139 2620 100.00 0.2697 0.2460 1.4590 131 2562 100.00 0.2808 0.2332 1.4790 142 2603 100.00 0.2523 0.2249 1.5001 132 2615 100.00 0.2552 0.2172 1.5225 130 2574 100.00 0.2673 0.2103 1.5463 144 2660 100.00 0.2503 0.2100 1.5717 138 2571 100.00 0.2304 0.2012 1.5988 135 2620 100.00 0.2216 0.1995 1.6278 136 2597 100.00 0.2203 0.1894 1.6592 139 2627 100.00 0.1941 0.1827 1.6930 137 2579 100.00 0.2243 0.1862 1.7298 133 2653 100.00 0.1777 0.1816 1.7701 144 2581 100.00 0.2026 0.1856 1.8143 131 2618 100.00 0.2176 0.1810 1.8634 140 2623 100.00 0.1793 0.1763 1.9182 136 2615 100.00 0.2010 0.1746 1.9801 140 2622 100.00 0.1829 0.1673 2.0509 136 2652 100.00 0.1656 0.1680 2.1330 135 2650 100.00 0.2069 0.1752 2.2300 138 2616 100.00 0.1948 0.1888 2.3476 139 2635 100.00 0.1683 0.1906 2.4946 140 2637 100.00 0.2024 0.1944 2.6871 134 2638 100.00 0.2023 0.1883 2.9574 139 2667 100.00 0.1981 0.1851 3.3850 138 2667 100.00 0.1764 0.1439 4.2633 142 2684 99.00 0.1681 0.1644 32.9841 147 2803 99.00 1.4049 50.0 5C2B 77347 0.037 1 22.5 6.5 99.9 0.542 1.4049 1.48 3.0 1 6.7 100 refinement PHENIX 1.8.2_1309 data reduction HKL-2000 data scaling SCALA phasing MOLREP scFv 3B4 anti-CXCL13 parental scFv - 3B4 1 N N 2 N N 2 N N 2 N N 3 N N H GLN 62 A GLN 62 HELX_P H GLN 65 A GLN 65 5 AA1 4 H GLU 74 A GLU 74 HELX_P H THR 76 A THR 76 5 AA2 3 H ARG 87 A ARG 87 HELX_P H THR 91 A THR 91 5 AA3 5 H GLN 1081 A GLN 223 HELX_P H GLU 1085 A GLU 227 5 AA4 5 disulf 2.047 H CYS 22 A SG CYS 22 1_555 H CYS 96 A SG CYS 96 1_555 disulf 2.046 B H CYS 1022 A SG CYS 164 1_555 H CYS 1090 A SG CYS 232 1_555 disulf 2.036 A H CYS 1022 A SG CYS 164 1_555 H CYS 1090 A SG CYS 232 1_555 IMMUNE SYSTEM anti-CXCL13, scFv, IMMUNE SYSTEM HV69D_HUMAN UNP 1 20 A0A0B4J2H0 QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAY MELSSLRSEDTAVYYCAR 5C2B PDB 1 99 5C2B A0A5C2GBJ8_HUMAN UNP 1 1 A0A5C2GBJ8 QSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLLIFDVSNRPSGVSYRFSGSKSGNTASLTISGL QAEDEADYYCSS 5C2B PDB 1 235 5C2B 20 117 5C2B 1 98 A0A0B4J2H0 H 1 1 98 99 142 5C2B 99 142 5C2B H 2 99 142 1 92 5C2B 1001 1092 A0A5C2GBJ8 H 3 143 234 1093 1112 5C2B 1093 1112 5C2B H 4 235 254 3 GLY conflict ALA 1012 5C2B H A0A5C2GBJ8 UNP 12 154 3 GLY conflict ALA 1031 5C2B H A0A5C2GBJ8 UNP 31 173 3 ASN conflict ASP 1033 5C2B H A0A5C2GBJ8 UNP 33 175 3 TYR conflict TRP 1034 5C2B H A0A5C2GBJ8 UNP 34 176 3 SER conflict ASN 1054 5C2B H A0A5C2GBJ8 UNP 54 196 3 TYR conflict HIS 1062 5C2B H A0A5C2GBJ8 UNP 62 204 4 4 5 5 4 3 anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel H GLN 3 A GLN 3 H GLN 6 A GLN 6 H VAL 18 A VAL 18 H SER 25 A SER 25 H THR 78 A THR 78 H LEU 83 A LEU 83 H VAL 68 A VAL 68 H ASP 73 A ASP 73 H GLU 10 A GLU 10 H LYS 12 A LYS 12 H THR 121 A THR 121 H VAL 125 A VAL 125 H ALA 92 A ALA 92 H ASP 104 A ASP 104 H GLY 107 A GLY 107 H PRO 110 A PRO 110 H ALA 58 A ALA 58 H TYR 60 A TYR 60 H LEU 45 A LEU 45 H ILE 51 A ILE 51 H TYR 32 A TYR 32 H GLN 39 A GLN 39 H ALA 92 A ALA 92 H ASP 104 A ASP 104 H ILE 116 A ILE 116 H TRP 117 A TRP 117 H SER 1009 A SER 151 H ALA 1012 A ALA 154 H THR 1105 A THR 247 H VAL 1109 A VAL 251 H ALA 1086 A ALA 228 H TYR 1093 A TYR 235 H VAL 1035 A VAL 177 H GLN 1040 A GLN 182 H LYS 1047 A LYS 189 H ILE 1050 A ILE 192 H SER 1009 A SER 151 H ALA 1012 A ALA 154 H THR 1105 A THR 247 H VAL 1109 A VAL 251 H ALA 1086 A ALA 228 H TYR 1093 A TYR 235 H TYR 1099 A TYR 241 H PHE 1101 A PHE 243 H ILE 1018 A ILE 160 H THR 1023 A THR 165 H THR 1072 A THR 214 H ILE 1077 A ILE 219 H PHE 1064 A PHE 206 H SER 1069 A SER 211 binding site for residue CL H 1201 H CL 1201 Software 2 binding site for residue CL H 1202 H CL 1202 Software 2 binding site for residue CL H 1203 H CL 1203 Software 2 H LYS 13 A LYS 13 2 1_555 H SER 16 A SER 16 2 1_555 H LYS 1047 A LYS 189 2 1_555 H SER 1061 A SER 203 2 1_555 H ALA 1045 A ALA 187 2 1_555 H HOH 1348 E HOH 2 1_555 20 C 2 2 21