Software Name Version Classification PHENIX(1.15.2_3472: ???)refinement PDB_EXTRACT3.27 data extraction HKL-2000data reduction HKL-2000data scaling PHENIXphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 4RLZResolution : 1.698→47.299 Å / SU ML : 0.14 / Cross valid method : THROUGHOUT / σ(F) : 1.36 / Phase error : 15.82 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.1746 3710 5.18 % Rwork 0.1427 - - obs 0.1443 71619 99.25 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELRefinement step Cycle : LAST / Resolution : 1.698→47.299 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 4730 0 0 771 5501
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.006 4888 X-RAY DIFFRACTION f_angle_d0.77 6692 X-RAY DIFFRACTION f_dihedral_angle_d7.185 3840 X-RAY DIFFRACTION f_chiral_restr0.054 743 X-RAY DIFFRACTION f_plane_restr0.006 884
LS refinement shell Show large table (7 x 26) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.698-1.7201 0.2264 119 0.1946 2341 X-RAY DIFFRACTION 90 1.7201-1.7437 0.2158 129 0.1874 2485 X-RAY DIFFRACTION 95 1.7437-1.7686 0.2012 154 0.1702 2537 X-RAY DIFFRACTION 99 1.7686-1.795 0.2224 143 0.1631 2550 X-RAY DIFFRACTION 99 1.795-1.823 0.2033 130 0.1568 2617 X-RAY DIFFRACTION 99 1.823-1.8529 0.2091 161 0.1563 2573 X-RAY DIFFRACTION 99 1.8529-1.8849 0.2052 155 0.1589 2556 X-RAY DIFFRACTION 100 1.8849-1.9192 0.1902 133 0.1554 2609 X-RAY DIFFRACTION 100 1.9192-1.9561 0.1972 148 0.1506 2628 X-RAY DIFFRACTION 100 1.9561-1.996 0.1585 156 0.1457 2567 X-RAY DIFFRACTION 100 1.996-2.0394 0.1848 131 0.1403 2623 X-RAY DIFFRACTION 100 2.0394-2.0869 0.2332 139 0.1362 2619 X-RAY DIFFRACTION 100 2.0869-2.139 0.1866 141 0.1406 2613 X-RAY DIFFRACTION 100 2.139-2.1969 0.1659 144 0.1369 2601 X-RAY DIFFRACTION 100 2.1969-2.2615 0.1579 124 0.1344 2638 X-RAY DIFFRACTION 100 2.2615-2.3345 0.1676 167 0.1399 2602 X-RAY DIFFRACTION 100 2.3345-2.4179 0.1729 169 0.1383 2632 X-RAY DIFFRACTION 100 2.4179-2.5148 0.1898 151 0.1438 2591 X-RAY DIFFRACTION 100 2.5148-2.6292 0.1729 132 0.1427 2653 X-RAY DIFFRACTION 100 2.6292-2.7678 0.172 132 0.1476 2656 X-RAY DIFFRACTION 100 2.7678-2.9412 0.1824 147 0.1464 2615 X-RAY DIFFRACTION 100 2.9412-3.1682 0.1832 128 0.1392 2679 X-RAY DIFFRACTION 100 3.1682-3.487 0.1657 137 0.1332 2689 X-RAY DIFFRACTION 100 3.487-3.9913 0.1709 129 0.1256 2685 X-RAY DIFFRACTION 100 3.9913-5.0277 0.1263 159 0.1189 2705 X-RAY DIFFRACTION 100 5.0277-47.299 0.159 152 0.159 2845 X-RAY DIFFRACTION 100
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 19) Hide large table ID L11 (°2 )L12 (°2 )L13 (°2 )L22 (°2 )L23 (°2 )L33 (°2 )S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2 )T12 (Å2 )T13 (Å2 )T22 (Å2 )T23 (Å2 )T33 (Å2 )Origin x (Å)Origin y (Å)Origin z (Å)1 1.2868 -0.3366 0.138 0.6854 0.3731 0.7659 -0.2143 0.1039 -0.0094 0.0534 0.115 0.0922 -0.2518 -0.1996 -0.0211 0.1387 0.0349 -0.0298 0.0801 0.0114 0.0845 68.0144 106.5258 22.1011 2 1.5318 -0.4021 -1.1252 1.0004 0.8188 2.5606 -0.1341 -0.1058 -0.1573 0.2089 0.0514 0.0346 0.2636 -0.0567 0.0172 0.1127 0.0202 -0.0023 0.0838 -0.0119 0.1197 73.1632 96.1313 28.05 3 3.0743 0.6686 2.9961 0.3085 1.204 4.7863 0.203 -0.2735 -0.4661 0.2544 0.0864 -0.1137 0.7503 -0.2037 -0.1651 0.4486 0.0175 -0.1732 0.2758 0.0312 0.2299 76.3747 99.113 44.4887 4 0.9795 -0.147 0.1618 1.0457 -0.0629 1.4623 -0.0269 -0.0279 0.0525 0.0234 0.0685 0.0085 -0.2139 0.0398 0.0036 0.0998 -0.0071 -0.0054 0.0638 -0.0132 0.0997 81.2504 108.7584 23.8464 5 3.0118 -0.0564 -1.2327 0.9977 0.0768 1.9302 -0.104 0.0856 -0.1836 -0.1373 0.1235 -0.2595 0.0214 0.3611 -0.0329 0.0656 0.0099 0.0364 0.2009 -0.0402 0.168 94.6028 96.5078 12.7412 6 0.5282 0.1131 0.187 0.5436 0.4072 1.6406 -0.004 0.1097 0.0226 -0.0048 0.1206 -0.2115 0.0412 0.3575 -0.0224 0.0695 0.0048 0.0045 0.1792 -0.0231 0.1474 95.3039 95.48 14.255 7 0.8029 -0.1194 -0.0323 1.1157 0.4164 1.2466 -0.04 -0.0604 0.1317 0.1198 0.1251 -0.2005 0.0236 0.2672 -0.0005 0.0697 0.0002 -0.0223 0.1188 -0.0201 0.1146 90.1568 100.5549 28.0441 8 0.5232 -0.2077 0.0683 1.0424 0.2821 1.3762 0.0073 -0.082 0.0119 0.0924 -0.0249 0.0593 -0.1157 -0.1461 -0.0256 0.0753 0.0204 -0.001 0.0723 -0.0128 0.0794 71.2776 105.0595 28.5339 9 1.6249 -0.142 0.0719 1.2427 0.5109 2.0999 -0.0292 -0.0934 -0.1667 0.1564 0.0208 0.0764 -0.0574 -0.2858 0.0145 0.1379 0.0455 0.0087 0.1394 -0.0004 0.124 64.8329 109.1506 35.4437 10 0.4428 -0.0373 0.6293 1.6618 0.1556 1.1474 -0.0192 -0.0228 0.1138 0.0263 -0.0387 -0.065 -0.1996 -0.0406 0.0031 0.1008 0.009 0.0111 0.0706 -0.0122 0.1 70.673 108.6155 6.9587 11 0.4923 -0.0966 0.5072 1.2126 -1.3283 1.8216 -0.0234 0.1308 0.0196 -0.1067 -0.1092 -0.3373 0.0689 0.2369 0.0389 0.1019 0.0176 0.0094 0.0987 -0.001 0.1224 78.6056 100.2614 0.8597 12 0.6093 0.8061 1.1606 1.0602 1.5463 2.3383 0.105 0.059 -0.2744 -0.183 0.1297 -0.2472 0.152 0.4702 -0.0813 0.2475 0.0212 0.0155 0.326 -0.0735 0.2286 74.5793 98.0788 -15.4467 13 0.709 0.0408 0.2004 1.0331 -0.1154 1.5215 0.0303 -0.0382 0.0874 -0.0393 0.0165 0.0209 0.0631 -0.2264 -0.0185 0.0677 -0.0117 -0.0036 0.0808 0.0073 0.0856 64.2071 96.7568 5.5954 14 0.963 0.0427 -0.2038 2.0203 -0.7547 0.9696 0.0275 -0.0058 -0.2849 -0.027 0.0085 -0.1272 0.2299 0.0377 -0.0392 0.1605 -0.0164 -0.0179 0.052 0.0207 0.1224 70.6585 78.2334 15.9686 15 0.7777 0.1643 0.2879 0.6218 -0.1781 1.4043 0.0634 -0.0425 -0.1486 -0.0064 0.0216 0.0404 0.2389 -0.0482 -0.0535 0.144 -0.0203 -0.0123 0.0563 0.0099 0.1028 71.9256 78.9582 14.4454 16 0.9977 -0.1254 0.2328 0.9042 -0.3723 1.2895 0.044 0.0863 -0.1133 -0.1185 0.018 0.1294 0.2157 -0.0737 -0.0212 0.1092 -0.0289 -0.0121 0.0629 0.0001 0.0839 68.5723 85.7579 0.916 17 0.6225 -0.3375 0.1002 0.6875 0.073 0.946 -0.0129 0.0688 0.0952 -0.089 0.0113 -0.0158 -0.0623 -0.0671 -0.0025 0.0754 0.0042 0.004 0.0793 0.0078 0.0924 69.9193 106.3659 -0.8655 18 1.4603 -0.3329 1.1397 0.0906 -0.2709 0.8689 -0.0084 0.4056 -0.2769 -0.2179 0.3584 -0.4041 -0.1501 0.8063 -0.1882 0.1754 -0.048 0.0192 0.2709 -0.0196 0.2657 80.1219 110.767 -7.3784 19 0.8084 -0.3045 0.248 0.9639 -0.2538 2.7895 0.0482 0.1607 0.1698 -0.2474 -0.1168 0.0481 -0.1685 -0.1723 0.023 0.1425 0.0264 -0.0034 0.1562 0.0347 0.1619 64.6245 115.0053 -6.4507
Refinement TLS group Show large table (4 x 19) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 4 through 20 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 21 through 30 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 31 through 35 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 36 through 61 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 62 through 72 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 88 through 174 )7 X-RAY DIFFRACTION 7 chain 'A' and (resid 175 through 212 )8 X-RAY DIFFRACTION 8 chain 'A' and (resid 213 through 270 )9 X-RAY DIFFRACTION 9 chain 'A' and (resid 271 through 317 )10 X-RAY DIFFRACTION 10 chain 'B' and (resid 4 through 20 )11 X-RAY DIFFRACTION 11 chain 'B' and (resid 21 through 30 )12 X-RAY DIFFRACTION 12 chain 'B' and (resid 31 through 35 )13 X-RAY DIFFRACTION 13 chain 'B' and (resid 36 through 61 )14 X-RAY DIFFRACTION 14 chain 'B' and (resid 62 through 73 )15 X-RAY DIFFRACTION 15 chain 'B' and (resid 87 through 174 )16 X-RAY DIFFRACTION 16 chain 'B'