Software Name Version Classification XDSdata reduction PHENIXrefinement PDB_EXTRACT3.15 data extraction XSCALEdata scaling PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : PDB entry 3ONU was used for GII.10 P domain (molecule 1) and recently deposited PDB entry 4X7F for Nano-85 (molecule 2)Resolution : 2.11→47.97 Å / SU ML : 0.23 / Cross valid method : FREE R-VALUE / σ(F) : 1.35 / Phase error : 24.17 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.2182 2327 5 % Rwork 0.1886 44237 - obs 0.1901 46564 95.77 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso max : 96.82 Å2 / Biso mean : 35.8568 Å2 / Biso min : 18.38 Å2 Refinement step Cycle : final / Resolution : 2.11→47.97 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 6413 0 36 290 6739 Biso mean - - 43.46 35.27 - Num. residues - - - - 847
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.002 6664 X-RAY DIFFRACTION f_angle_d0.701 9088 X-RAY DIFFRACTION f_chiral_restr0.029 1005 X-RAY DIFFRACTION f_plane_restr0.004 1197 X-RAY DIFFRACTION f_dihedral_angle_d13.65 2379
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Number Refine-ID Rms Type 1 1 A2772 X-RAY DIFFRACTION 3.233 TORSIONAL1 2 C2772 X-RAY DIFFRACTION 3.233 TORSIONAL2 1 B1026 X-RAY DIFFRACTION 3.233 TORSIONAL2 2 D1026 X-RAY DIFFRACTION 3.233 TORSIONAL
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 17
Show large table (7 x 17) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)2.1102-2.1533 0.3098 125 0.2652 2382 2507 89 2.1533-2.2001 0.2952 140 0.2688 2672 2812 99 2.2001-2.2513 0.3011 133 0.3114 2567 2700 93 2.2513-2.3076 0.3219 132 0.2804 2503 2635 94 2.3076-2.37 0.2673 141 0.2283 2668 2809 98 2.37-2.4397 0.2732 139 0.2335 2643 2782 98 2.4397-2.5185 0.2515 138 0.2298 2629 2767 97 2.5185-2.6085 0.2657 142 0.218 2685 2827 98 2.6085-2.7129 0.2637 139 0.2203 2636 2775 97 2.7129-2.8364 0.244 138 0.2086 2615 2753 98 2.8364-2.9859 0.2374 139 0.1983 2646 2785 98 2.9859-3.1729 0.2471 138 0.1922 2621 2759 97 3.1729-3.4178 0.2102 138 0.1807 2632 2770 97 3.4178-3.7617 0.1868 137 0.1631 2601 2738 95 3.7617-4.3057 0.171 136 0.1465 2576 2712 95 4.3057-5.4235 0.1497 135 0.1347 2567 2702 94 5.4235-47.9848 0.1896 137 0.164 2594 2731 93
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 34) 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 0.2869 -0.3066 -0.4879 0.4212 0.7834 1.4596 -0.1089 -0.0195 -0.1032 0.0191 -0.0015 0.0771 0.1741 -0.0775 -0.0007 0.2216 -0.0065 0.0434 0.2199 0.0121 0.2727 57.8074 24.7949 29.7469 2 0.6972 -0.1893 -0.1745 0.921 0.1176 0.4689 -0.0936 -0.0914 0.0077 0.0391 -0.0495 0.2124 0.0713 -0.2197 -0 0.2081 0.0259 0.0397 0.2844 0.0044 0.2242 52.4144 28.5115 41.702 3 0.9994 -0.1644 0.0366 0.7735 0.2199 0.7379 -0.0778 -0.1576 -0.1519 0.1671 0.0476 0.0751 0.2192 -0.0971 -0 0.2625 0.0109 0.0657 0.259 0.0369 0.2534 59.5029 19.0604 37.4263 4 0.9276 -0.7782 -0.1185 0.7524 0.1323 0.6286 -0.0515 -0.1345 -0.1206 0.0046 0.0198 0.1331 -0.1395 0.0448 -0 0.2417 -0.0418 0.0342 0.2131 -0.0202 0.2525 66.4777 22.2701 15.5294 5 0.0743 -0.0266 -0.1764 0.4311 -0.0526 0.9388 -0.0546 0.36 -0.1421 -0.1018 0.0105 -0.0937 0.1045 0.1394 0 0.2487 0.0228 0.0085 0.2258 -0.0152 0.3353 72.4802 13.2027 17.8441 6 0.1292 -0.0432 -0.2773 0.1499 0.2076 0.6486 -0.0171 -0.0402 -0.1571 0.0249 0.0983 0.0466 0.0778 0.0598 -0 0.2545 0.0112 -0.003 0.2321 -0.0253 0.257 70.0084 12.9867 8.8576 7 1.1866 0.3594 0.1733 0.1166 0.0696 0.0312 0.3064 0.1779 -0.3159 -0.6208 0.0321 -0.0579 -0.1023 -0.3922 0.0191 0.5624 0.1303 -0.0287 0.5886 0.0173 0.2628 69.4024 2.2632 -13.0094 8 0.0058 -0.0048 -0.0289 0.0033 0.0112 0.0549 0.2291 0.0696 -0.0188 -0.2773 0.1479 0.0618 0.1783 0.4112 0.0001 0.5291 0.0215 -0.0163 0.393 -0.0994 0.5015 76.1057 -19.2509 -7.6349 9 2.4382 0.9197 -0.2615 0.3631 -0.082 0.0761 0.0125 -0.0326 -0.2622 -0.1489 -0.0389 -0.3682 -0.2088 0.0587 -0.0733 0.4586 0.0335 -0.0096 0.3892 -0.0543 0.1625 75.2645 -2.167 -9.2971 10 0.0953 -0.0477 -0.0612 0.0698 0.1187 0.1624 0.2416 -0.0261 -0.095 -0.3195 -0.258 0.6082 -0.0712 -0.1739 -0.0036 0.3278 0.0624 0.0049 0.2479 0.0005 0.4335 69.1312 2.3579 -3.5616 11 0.0583 -0.0778 0.0162 0.0782 -0.029 0.1576 0.1422 -0.0372 -0.354 0.4482 -0.0003 0.3131 0.2553 -0.1891 -0.0003 0.2609 -0.0472 -0.0206 0.2812 -0.0238 0.3862 64.3447 -7.6771 0.1193 12 0.209 -0.0285 0.134 0.253 0.1454 0.081 -0.0802 0.0417 -0.0794 -0.032 0.0834 -0.2394 0.081 0.1299 0 0.2977 0.0285 0.0278 0.3072 0.041 0.316 74.5737 -5.0853 4.3309 13 2.1634 -0.196 0.4215 0.3817 -0.0382 0.0914 0.3445 0.127 -0.2811 0.179 -0.248 0.037 -0.277 0.5263 0.1218 0.4077 -0.0065 0.0687 0.3626 -0.0039 0.1519 78.3423 -0.89 -5.3817 14 0.4925 -0.3982 0.0757 0.4169 -0.0047 0.0231 0.3287 -0.4801 -0.83 0.8652 0.2263 0.6674 0.2005 -0.5295 -0.003 0.4448 -0.0302 -0.059 0.4222 0.047 0.483 71.9309 -18.7348 -0.6773 15 0.0335 0.049 0.0902 0.0614 0.0906 0.0115 0.2287 0.1764 -0.1169 -0.5228 -0.2596 0.5251 -0.3274 -0.0289 0.0004 0.3477 -0.002 -0.0452 0.2818 -0.0464 0.3436 66.4401 0.0852 -4.7414 16 0.0352 -0.0848 -0.0052 1.1861 0.069 0.1106 0.253 0.0464 -0.0287 0.0027 -0.259 0.9712 -0.1908 -0.3336 0.0182 0.3247 -0.0144 -0.0447 0.2868 -0.0566 0.2331 63.4314 10.1318 -4.5713 17 0.0161 -0.0164 0.0289 0.0606 0.0347 0.0654 -0.1572 0.0011 -0.2826 0.2651 -0.1508 -0.1222 0.3443 0.0112 -0.0005 0.5018 0.0413 -0.0938 0.3972 -0.0627 0.5077 70.1365 -19.3834 -9.1061 18 0.2242 0.0728 0.6955 0.2279 -0.2512 1.1222 -0.0992 -0.1137 0.0736 -0.0762 0.0703 -0.0382 -0.1357 0.0305 -0.0018 0.2416 -0.0007 -0.0177 0.234 -0.0161 0.2168 69.1064 43.1691 26.9074 19 0.3785 -0.204 0.1765 1.3734 -0.489 0.381 -0.0642 -0.11 0.0244 0.1402 -0.0163 -0.0865 -0.0624 0.1775 -0 0.2194 0.0199 -0.0512 0.3147 0.003 0.2676 77.1575 37.5268 42.9303 20 0.2326 -0.2254 0.1194 0.5895 -0.1615 0.6311 -0.009 0.0031 0.2737 0.133 0.0037 -0.0715 -0.2167 0.1202 -0 0.3017 0.0043 -0.0579 0.2611 -0.0271 0.3166 69.4005 52.5846 32.1582 21 0.5476 -0.8255 0.0091 0.9389 -0.0493 0.2838 -0.0178 -0.0401 0.1773 -0.0646 0.0195 -0.1016 0.1626 -0.1041 0 0.2568 -0.0407 -0.0462 0.2469 0.0362 0.2871 63.3735 44.2005 15.5573 22 0.0308 -0.1438 -0.1807 0.5173 0.2501 0.6584 -0.1746 0.2482 0.1722 -0.2076 0.26 0.1298 -0.1692 -0.2985 0.0001 0.245 0.0281 -0.0005 0.269 0.0206 0.3362 57.9342 53.1937 17.6365 23 0.1705 -0.0041 0.2408 0.1947 -0.3422 0.6391 -0.0127 0.1597 0.1896 -0.0253 0.118 -0.1355 -0.0142 -0.121 0 0.3075 0.0234 -0.0002 0.2511 0.0144 0.3082 59.8152 53.5003 8.8846 24 1.5997 0.2656 -0.3062 0.5847 0.0226 0.0731 0.5512 0.6892 0.4945 -0.0395 0.0148 0.19 0.3472 0.6554 0.043 0.7544 0.1808 0.119 0.6338 0.0036 0.4142 60.4237 64.2841 -12.963 25 0.0222 0.0086 -0.0096 -0.0021 -0.0072 0.0798 0.388 -0.0333 0.4583 -0.1192 0.0842 -0.1558 0.0748 -0.1909 -0.0001 0.4486 0.0514 0.066 0.3125 0.1415 0.6128 53.7862 85.7438 -7.5868 26 0.0091 0.0225 0.0372 0.0327 0.0207 0.0573 0.2836 0.395 -0.2317 -0.1211 -0.1999 -0.0802 0.1541 -0.046 -0.0002 0.513 0.0958 0.0007 0.4527 0.022 0.2958 54.5832 68.6991 -9.1369 27 0.1717 -0.0269 0.0972 0.0521 -0.0847 0.1817 0.1576 0.0141 -0.0275 -0.3619 -0.0859 -0.5011 -0.0221 0.2096 0.0004 0.3738 0.0458 0.0021 0.2771 -0.0023 0.4208 60.8755 63.5027 -3.436 28 0.0529 -0.0092 0.0517 0.0326 0.0155 0.069 -0.0545 -0.0527 0.466 0.2075 0.1565 -0.3035 -0.1933 0.1378 -0.0004 0.3089 -0.0271 0.0148 0.3178 -0.0176 0.4836 66.0541 74.331 -0.1015 29 0.1815 0.0162 -0.1774 0.2627 -0.1496 0.0945 -0.1247 0.0598 -0.0571 0.0601 0.2637 0.1642 -0.0639 -0.0878 -0.0001 0.294 0.0039 -0.0296 0.3005 -0.0404 0.349 55.2882 71.5801 4.352 30 0.3931 0.062 -0.3714 0.0129 -0.0983 0.4552 0.1395 0.3034 0.1383 0.3025 0.045 -0.4179 0.16 -0.0335 0.0001 0.337 0.0171 -0.0451 0.3524 -0.0333 0.4057 54.1403 74.9864 -3.4584 31 0.2197 -0.0278 -0.1389 0.0358 0.0257 0.0779 0.0642 0.1804 0.273 -0.6076 -0.0886 -0.5866 0.4196 0.1715 0.0002 0.4228 0.021 0.0554 0.3525 0.021 0.3584 63.398 66.4006 -4.7354 32 0.165 -0.115 0.1903 0.1858 -0.2011 0.2555 -0.2695 0.4722 0.0256 -0.1835 -0.204 -0.3276 0.09 0.0159 -0.0241 0.3378 -0.0021 -0.019 0.2585 -0.0892 0.3268 66.2231 48.2597 -0.5984 33 0.0237 0.0265 0.0316 0.0551 0.0646 0.1022 0.0586 -0.3166 0.591 0.4375 0.0802 -0.4154 -0.45 0.4494 0.0138 0.4308 0.0253 0.1326 0.4351 -0.0021 0.4482 66.3113 64.9416 -8.5705 34 0.019 -0.0062 -0.0332 0.0538 -0.025 0.0526 0.0925 -0.0359 -0.0254 0.3839 0.0313 -0.1519 -0.1739 0.0363 0.0002 0.3797 0.026 0.0819 0.365 0.1807 0.5704 59.9708 84.9413 -8.8728
Refinement TLS group Show large table (6 x 34) 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 224 through 317 )A0 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 318 through 380 )A0 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 381 through 455 )A0 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 456 through 491 )A0 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 492 through 520 )A0 6 X-RAY DIFFRACTION 6 chain 'A' and (resid 521 through 538 )A0 7 X-RAY DIFFRACTION 7 chain 'B' and (resid 1 through 7 )B0 8 X-RAY DIFFRACTION 8 chain 'B' and (resid 8 through 17 )B0 9 X-RAY DIFFRACTION 9 chain 'B' and (resid 18 through 26 )B0 10 X-RAY DIFFRACTION 10 chain 'B' and (resid 27 through 39 )B0 11 X-RAY DIFFRACTION 11 chain 'B' and (resid 40 through 52 )B0 12 X-RAY DIFFRACTION 12 chain 'B' and (resid 53 through 72 )B0 13 X-RAY DIFFRACTION 13 chain 'B' and (resid 73 through 82 )B