Software Name Version Classification XDSdata reduction PHENIXrefinement PDB_EXTRACT3.15 data extraction XSCALEdata scaling PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : As search models for molecular replacement PDB code 3ONU was used for GII.10 P domain (molecule 1) and PDB code 3P0G for Nano-25 (molecule 2)Resolution : 1.7→46.587 Å / SU ML : 0.18 / Cross valid method : FREE R-VALUE / σ(F) : 1.09 / Phase error : 17.47 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.1868 8313 5.02 % Rwork 0.1599 157298 - obs 0.1612 88133 97.44 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso max : 94.62 Å2 / Biso mean : 32.6161 Å2 / Biso min : 13.2 Å2 Refinement step Cycle : final / Resolution : 1.7→46.587 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 6330 0 108 464 6902 Biso mean - - 42.22 38.57 - Num. residues - - - - 836
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.01 6614 X-RAY DIFFRACTION f_angle_d1.191 8997 X-RAY DIFFRACTION f_chiral_restr0.06 1001 X-RAY DIFFRACTION f_plane_restr0.007 1182 X-RAY DIFFRACTION f_dihedral_angle_d12.468 2323
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Number Refine-ID Rms Type 1 1 A2724 X-RAY DIFFRACTION 5.986 TORSIONAL1 2 B2724 X-RAY DIFFRACTION 5.986 TORSIONAL2 1 C936 X-RAY DIFFRACTION 5.986 TORSIONAL2 2 D936 X-RAY DIFFRACTION 5.986 TORSIONAL
LS refinement shell Show large table (7 x 30) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.6984-1.7177 0.2919 231 0.2763 4407 X-RAY DIFFRACTION 83 1.7177-1.7379 0.2851 275 0.2549 5116 X-RAY DIFFRACTION 95 1.7379-1.7591 0.2773 276 0.2382 5195 X-RAY DIFFRACTION 96 1.7591-1.7814 0.2591 274 0.2189 5223 X-RAY DIFFRACTION 98 1.7814-1.8048 0.2516 285 0.2052 5351 X-RAY DIFFRACTION 99 1.8048-1.8296 0.2059 278 0.1813 5328 X-RAY DIFFRACTION 99 1.8296-1.8557 0.2203 279 0.1809 5267 X-RAY DIFFRACTION 99 1.8557-1.8834 0.2132 283 0.1691 5335 X-RAY DIFFRACTION 99 1.8834-1.9128 0.1863 279 0.1689 5287 X-RAY DIFFRACTION 98 1.9128-1.9442 0.2074 280 0.162 5311 X-RAY DIFFRACTION 99 1.9442-1.9777 0.2073 286 0.1649 5342 X-RAY DIFFRACTION 98 1.9777-2.0137 0.1775 270 0.1589 5242 X-RAY DIFFRACTION 98 2.0137-2.0524 0.1922 285 0.1531 5370 X-RAY DIFFRACTION 98 2.0524-2.0943 0.188 279 0.1566 5241 X-RAY DIFFRACTION 98 2.0943-2.1398 0.1928 278 0.1559 5344 X-RAY DIFFRACTION 99 2.1398-2.1896 0.1929 274 0.152 5236 X-RAY DIFFRACTION 98 2.1896-2.2444 0.1724 280 0.1559 5333 X-RAY DIFFRACTION 98 2.2444-2.3051 0.1761 275 0.156 5237 X-RAY DIFFRACTION 98 2.3051-2.3729 0.1949 276 0.1556 5249 X-RAY DIFFRACTION 98 2.3729-2.4495 0.1877 274 0.1562 5254 X-RAY DIFFRACTION 97 2.4495-2.537 0.1874 274 0.1578 5230 X-RAY DIFFRACTION 98 2.537-2.6386 0.2054 277 0.1577 5276 X-RAY DIFFRACTION 98 2.6386-2.7587 0.1951 281 0.1559 5264 X-RAY DIFFRACTION 98 2.7587-2.9041 0.1999 282 0.1607 5310 X-RAY DIFFRACTION 98 2.9041-3.086 0.2028 280 0.1586 5272 X-RAY DIFFRACTION 98 3.086-3.3242 0.1759 278 0.156 5252 X-RAY DIFFRACTION 98 3.3242-3.6586 0.1651 276 0.1465 5241 X-RAY DIFFRACTION 98 3.6586-4.1877 0.1536 281 0.1454 5324 X-RAY DIFFRACTION 98 4.1877-5.2749 0.1508 285 0.1401 5262 X-RAY DIFFRACTION 98 5.2749-46.6047 0.2097 282 0.1829 5199 X-RAY DIFFRACTION 97
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 29) 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 1.4665 -0.5309 -0.2817 1.4668 -0.5618 1.7263 0.0219 -0.2661 0.0271 0.0534 0.0407 0.0639 -0.1072 0.123 -0.0587 0.1235 -0.0379 -0.0042 0.1921 -0.0112 0.1364 3.682 -4.6621 -21.8344 2 1.3077 -0.1569 0.1833 0.8426 -0.6537 2.2858 0.0544 -0.1075 0.1989 0.1291 0.0431 0.1043 -0.5627 -0.0731 -0.0699 0.2658 0.0112 0.0611 0.1332 -0.0337 0.2053 -2.6854 9.5125 -26.6297 3 1.8728 -1.2735 -1.2173 1.9357 0.3441 2.5519 0.2353 -0.5447 0.1229 0.6368 -0.117 0.3207 -0.4441 -0.0979 -0.066 0.2794 -0.0124 0.045 0.3487 -0.0153 0.2108 1.5508 -1.9688 -10.7192 4 1.0711 -0.1072 -0.3129 0.9186 -0.7122 1.7399 0.0307 -0.3692 -0.0593 0.0542 -0.0635 -0.1877 -0.0441 0.398 0.0125 0.1372 -0.0308 -0.0201 0.3226 0.0379 0.1677 14.7539 -8.6294 -19.586 5 5.0832 2.5531 -1.5171 2.5323 -1.1647 2.325 -0.0106 -0.3016 -0.3685 -0.3585 -0.3141 -0.3402 0.2824 0.9411 0.3034 0.3117 0.0716 0.0245 0.5048 0.1331 0.3364 21.3422 -23.9847 -22.619 6 2.53 0.1759 -0.4954 2.1037 -0.1519 1.5993 -0.0654 -0.0322 -0.0684 0.108 -0.1151 -0.3699 0.026 0.9093 0.0732 0.1582 -0.0381 -0.0363 0.5833 0.1291 0.2451 23.5536 -15.2886 -17.4735 7 1.8785 0.4881 0.6284 2.3017 -1.917 4.341 0.2154 -0.3659 -0.3284 -0.138 -0.167 -0.2454 0.4084 0.7263 -0.0422 0.2455 0.0788 0.0239 0.4877 0.1114 0.3194 22.5102 -24.6564 -16.3733 8 2.0685 0.1115 -0.5642 1.0342 0.8556 2.0077 0.0322 0.0186 0.0326 -0.1279 -0.0326 0.037 0.0377 -0.0552 -0.003 0.1951 -0 -0.0062 0.1179 0.0115 0.1628 2.907 -11.0003 -45.6493 9 1.6911 1.1238 -0.155 4.3229 -0.1275 1.2098 0.1 -0.1231 0.1185 -0.095 -0.033 -0.1357 -0.1828 0.267 -0.0974 0.1587 -0.0405 0.0215 0.182 -0.0031 0.1977 17.0882 -3.073 -41.6886 10 1.4268 0.7342 -0.0211 2.9197 -0.0174 2.5236 0.1222 0.0995 0.2657 -0.0767 -0.1104 -0.4185 -0.4987 0.3507 -0.0467 0.289 -0.1129 0.0732 0.3269 -0.0242 0.3866 22.7162 7.4535 -41.3893 11 1.0172 0.0985 -0.4495 1.5872 0.5288 2.1757 0.2472 -0.2025 0.2019 -0.0757 -0.0877 -0.2862 -0.5519 0.3825 -0.1013 0.2946 -0.1058 0.0655 0.2003 -0.0202 0.2546 16.7447 7.8188 -41.5247 12 1.6771 0.3316 -0.2694 1.5936 -0.2027 1.467 0.2268 -0.0617 0.3195 -0.2128 -0.0821 -0.2157 -0.5487 0.1887 -0.07 0.3224 -0.0581 0.0883 0.1335 -0.0136 0.2545 12.4406 8.0134 -46.2111 13 0.8727 0.231 -0.3187 0.4097 0.5978 1.2576 0.0586 0.0354 -0.0363 -0.0502 -0.036 0.0391 -0.0081 -0.0587 -0.0405 0.197 -0.0087 -0.0011 0.1261 -0.0018 0.1848 2.8183 -9.0994 -47.0485 14 4.2137 -1.2154 0.4247 3.7631 0.2049 2.4849 -0.0919 -0.1732 -0.1783 0.1288 0.0152 0.4097 0.1425 -0.3205 0.0816 0.2291 -0.0198 -0.007 0.1633 -0.0124 0.2251 -2.2092 -20.5596 -47.9641 15 1.1832 -0.3082 -0.1957 0.8795 0.8561 2.4251 -0.1345 0.04 -0.1086 0.0374 0.0531 0.0476 0.4124 -0.1861 0.0659 0.2848 -0.0372 0.0096 0.179 0.0008 0.2545 -1.3906 -25.785 -51.3771 16 4.1957 -2.4714 2.4507 4.8296 -1.3082 5.888 -0.1645 -0.2533 -0.0133 -0.0437 0.0249 -0.211 -0.5064 0.3242 0.1577 0.4295 0.0503 -0.1239 0.7348 -0.0344 0.3998 10.7543 -11.5779 6.5807 17 1.8656 -1.6737 1.1959 1.6939 -0.4719 2.0495 -0.1903 -0.5326 -0.2854 0.4402 0.4248 0.2377 -0.2159 -0.554 -0.1253 0.353 0.0769 0.0216 0.8049 0.2507 0.3956 11.69 -26.6286 15.2275 18 3.0626 1.0352 0.7792 7.1481 5.3087 3.9571 -0.1977 -0.0822 0.1718 0.3176 0.0889 0.3433 -0.1158 -0.0048 0.1072 0.2746 0.0639 0.0183 0.4227 0.09 0.238 4.3983 -14.009 -2.2081 19 7.6565 -2.5091 3.9967 4.0084 -2.9239 7.9853 0.3417 0.0647 0.2208 0.0809 -0.4647 -0.1726 0.0053 0.3449 0.0191 0.2721 -0.0721 -0.0552 0.4785 0.1149 0.2289 15.8619 -21.187 3.0679 20 3.7929 1.1253 1.9001 3.2571 1.4233 3.6032 0.1804 0.0546 -0.149 0.1394 -0.0952 -0.6353 -0.0326 0.881 -0.037 0.1596 -0.0274 -0.2288 0.9002 0.3133 0.2008 20.5297 -22.873 3.3152 21 3.9523 -4.2313 1.1846 7.0438 -1.5385 1.2052 0.1855 0.4502 -0.1721 -0.9226 -0.135 0.9001 -0.1474 -0.0629 0.0156 0.4742 -0.0809 -0.2117 0.5146 0.1445 0.4575 8.328 -27.4247 -4.183 22 2.4324 -1.3478 0.6208 3.155 -0.4561 1.151 0.4277 -0.2393 -0.2631 -0.4329 -0.0175 0.4361 -0.0643 -0.3009 -0.3369 0.3199 -0.0205 -0.0501 0.5794 0.242 0.4563 9.1426 -28.0783 4.2124 23 3.4128 0.435 2.7219 1.6479 -1.077 4.0295 0.1839 -0.1357 -0.5454 0.0329 0.1793 0.0694 0.3256 0.0606 -0.2729 0.2834 -0.0605 -0.0384 0.7144 0.2282 0.33 14.4175 -29.4815 11.0551 24 0.6784 -1.0565 0.6115 1.7784 -1.2431 1.6128 -0.2334 -0.2939 -0.0125 0.5273 0.2455 -0.0854 -0.4796 -0.2235 0.0297 0.3422 0.0133 -0.0872 0.6659 0.0765 0.2808 17.8267 -19.0291 9.7463 25 2.9891 1.5863 1.4878 8.0518 3.2066 3.6368 -0.3392 0.7411 -0.1858 -0.3348 0.2055 -0.1571 -0.3444 -0.1709 0.1512 0.3798 -0.0946 0.0923 0.4309 -0.0679 0.2383 8.1274 -19.8707 -80.1418 26 5.6698 1.3348 -1.2966 3.3453 -3.2288 3.1407 0.1726 -0.1026 0.6249 -0.0559 0.1164 -0.1041 -0.9092 0.6139 -0.2486 0.3931 -0.0789 0.0349 0.3157 -0.0808 0.3194 13.2672 -11.1287 -64.459 27 5.0129 1.0661 1.5855 3.2372 0.7809 4.1861 -0.2075 0.2276 0.0969 -0.2867 0.0367 0.3116 -0.1174 -0.4229 0.1364 0.2187 -0.0171 -0.0066 0.2139 -0.0298 0.173 1.4071 -21.6066 -70.5187 28 5.7793 0.647 1.0385 2.812 0.8501 5.1951 -0.2294 -0.3353 -0.4232 0.2859 0.1105 -0.0857 0.4738 0.2694 0.1232 0.2993 0.0189 0.0695 0.2049 -0.0277 0.3468 10.533 -27.2437 -68.519 29 2.997 0.0687 0.0887 2.2084 0.6751 4.056 -0.2347 0.6406 -0.278 -0.2815 0.0439 -0.0244 -0.1565 -0.2894 0.1594 0.2578 -0.0493 0.0437 0.3193 -0.0667 0.2029 5.0808 -20.8015 -76.1196
Refinement TLS group Show large table (6 x 29) Hide large table ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 225 through 332 )A0 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 333 through 406 )A0 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 407 through 427 )A0 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 428 through 472 )A0 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 473 through 492 )A0 6 X-RAY DIFFRACTION 6 chain 'A' and (resid 493 through 521 )A0 7 X-RAY DIFFRACTION 7 chain 'A' and (resid 522 through 538 )A0 8 X-RAY DIFFRACTION 8 chain 'B' and (resid 224 through 265 )B0 9 X-RAY DIFFRACTION 9 chain 'B' and (resid 266 through 294 )B0 10 X-RAY DIFFRACTION 10 chain 'B' and (resid 298 through 317 )B0 11 X-RAY DIFFRACTION 11 chain 'B' and (resid 318 through 379 )B0 12 X-RAY DIFFRACTION 12 chain 'B' and (resid 380 through 426 )B0 13 X-RAY DIFFRACTION 13 chain 'B' and (resid 427 through 472 )B