Software Name Version Classification PHENIX1.17.1_3660refinement XDSdata reduction XSCALEdata scaling PHASERphasing PDB_EXTRACT3.25 data extraction
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 3GBNResolution : 2.85→35.26 Å / SU ML : 0.37 / Cross valid method : THROUGHOUT / σ(F) : 1.36 / Phase error : 24.95 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.2475 1613 4.78 % Rwork 0.2086 32115 - obs 0.2104 33728 99.87 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso max : 260.63 Å2 / Biso mean : 94.4453 Å2 / Biso min : 31.13 Å2 Refinement step Cycle : final / Resolution : 2.85→35.26 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 5864 0 57 38 5959 Biso mean - - 117.44 59.14 - Num. residues - - - - 790
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.005 6066 X-RAY DIFFRACTION f_angle_d0.702 8273 X-RAY DIFFRACTION f_dihedral_angle_d18.622 2094 X-RAY DIFFRACTION f_chiral_restr0.047 938 X-RAY DIFFRACTION f_plane_restr0.006 1069
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Rfactor Rfree error : 0 / Total num. of bins used : 12
Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)2.85-2.93 0.326 154 0.294 2665 2819 100 2.93-3.03 0.3328 127 0.264 2639 2766 100 3.03-3.14 0.2848 112 0.2464 2665 2777 100 3.14-3.26 0.2591 160 0.2355 2645 2805 100 3.26-3.41 0.3094 125 0.251 2662 2787 100 3.41-3.59 0.2744 118 0.2413 2680 2798 100 3.59-3.82 0.2453 133 0.2093 2672 2805 100 3.82-4.11 0.2374 116 0.1905 2695 2811 100 4.11-4.52 0.2159 164 0.1669 2632 2796 100 4.52-5.17 0.2078 146 0.1732 2682 2828 100 5.18-6.51 0.2631 124 0.2102 2723 2847 100 6.51-35.26 0.2388 134 0.2118 2755 2889 99
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 24) 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 2.2988 -2.1191 2.1289 2.654 -2.4048 3.8238 0.1076 0.1782 0.3634 -0.1117 -0.3323 -0.6887 0.3447 0.6402 0.2145 0.3987 -0.012 0.049 0.6012 -0.0293 0.5737 -46.1549 -34.7011 25.0569 2 2.3018 -1.4914 2.0198 1.5047 -2.8239 5.9967 0.4598 0.8251 -0.1822 -0.0455 -0.4671 -0.8838 0.892 1.4975 0.3137 0.793 0.1879 -0.1377 1.1419 0.0125 1.2255 -26.9636 -51.2237 44.7355 3 0.3037 -0.7695 -0.2443 2.5277 -0.1436 3.3009 -0.0244 -1.2943 -0.3792 0.1941 -0.2156 -1.1165 0.2822 1.326 0.2726 0.6898 0.0404 -0.2414 1.8261 0.3154 1.3042 -17.28 -53.0151 55.825 4 5.5459 -0.7221 0.7427 4.6008 -0.9141 5.3548 -0.2859 -1.2045 -0.8174 0.8303 -0.5175 -0.8134 1.1734 1.5949 0.4162 1.1398 0.5194 -0.1367 1.5504 0.3022 1.1896 -22.8759 -58.093 62.8146 5 3.6213 -1.7047 2.756 3.1498 -3.0963 4.0973 -0.1627 0.1397 0.9514 -0.0151 -0.4279 -0.7406 0.0747 1.4298 0.7968 0.6034 0.0518 -0.0493 0.9802 0.0443 0.9433 -31.4006 -40.0521 39.829 6 4.1838 -3.6394 3.477 4.025 -4.0799 4.0274 -0.0224 0.1461 0.4026 0.0186 -0.2365 -0.4376 0.0096 0.5511 0.1319 0.3397 0.0304 0.0531 0.4832 -0.0341 0.5428 -51.5571 -34.3601 25.5266 7 3.9178 -0.1174 -1.3753 4.8577 -2.8705 5.9661 -0.2519 0.6573 -0.2216 -0.6722 0.066 -0.0204 0.6128 -0.1354 0.187 0.4077 0.0027 0.1093 0.409 -0.0948 0.4259 -69.9639 -19.135 10.2759 8 2.6187 -2.4536 2.2154 4.8736 -2.7124 4.2986 -0.2942 0.0034 0.2351 0.2998 0.1816 -0.2301 -0.6504 -0.3481 0.0878 0.3088 -0.1028 0.0843 0.4442 -0.0703 0.4438 -64.5786 -12.973 16.354 9 0.2684 -1.1885 0.931 5.5304 -4.1492 3.2258 -0.2319 -1.2413 0.9798 1.7735 0.4084 -1.6448 -1.3717 0.4556 0.4147 1.5298 0.2555 -0.0968 1.3686 -0.1624 0.8545 -49.8735 -31.7679 38.8415 10 0.9672 -1.6518 1.553 5.2187 -4.17 4.2876 -0.1822 -0.1552 -0.0003 0.224 0.1839 -0.141 0.0247 -0.183 -0.0597 0.4645 -0.0485 0.0198 0.4279 -0.0752 0.4269 -63.2121 -33.3868 29.2982 11 2.4412 -0.5803 2.4094 7.2811 -3.2115 8.3518 0.3869 1.2267 0.677 -0.7098 0.1078 0.0334 -0.5487 -0.7121 -0.585 0.5571 0.0928 0.0693 0.7431 0.0952 0.6182 -79.803 -5.9116 1.6805 12 2.6737 0.5563 -2.9217 3.7249 -5.3747 9.516 0.7094 0.2689 1.182 0.4635 -0.1584 -1.1916 -1.7392 0.1346 -0.0877 0.8109 0.042 0.1037 0.5606 0.0322 0.7089 -71.638 0.3921 7.4683 13 3.9192 0.058 -2.3574 8.7294 -0.0266 4.5746 0.3483 0.2488 0.9247 -0.1628 0.818 1.0069 -2.0993 -1.6555 -0.8368 1.0548 0.4416 0.1381 0.9362 0.1013 0.8775 -82.8222 4.5213 6.8309 14 3.9658 4.2909 0.1015 6.9629 -2.0024 7.3064 -0.0278 -0.6385 -1.0094 0.2696 -0.2132 -0.4473 0.0602 1.1631 0.1198 0.3867 -0.0411 -0.0868 0.7606 0.036 0.5774 -34.0127 -10.0083 24.8201 15 6.3299 1.7666 -0.9807 4.0597 -1.0033 2.1047 -0.101 0.0904 -0.45 -0.239 0.0463 -0.2645 -0.0158 0.2483 0.059 0.3789 -0.0385 0.0775 0.4598 -0.1519 0.5367 -43.7426 -10.6101 19.1078 16 7.1358 3.3993 -0.0521 4.4874 -0.7978 4.5135 -0.2001 -0.1073 0.2206 0.0703 0.0938 -0.2198 -0.2527 0.5856 0.0495 0.4235 -0.0749 0.0224 0.4061 -0.1131 0.4424 -38.6945 -4.455 20.6368 17 9.9371 -0.2975 1.3799 2.5659 2.4353 2.6047 -0.1689 0.1928 0.1147 1.8065 0.8046 0.766 0.802 -0.1956 -0.4331 1.0399 -0.1112 0.1837 1.8355 -0.3642 1.2662 -12.6996 -3.4889 27.2003 18 7.8779 -4.5228 0.4813 5.2403 -0.6668 1.4956 -0.6403 0.3553 0.6774 1.5529 -1.9183 0.8172 1.8648 -0.6507 2.2191 1.3064 -0.5368 0.19 1.8849 -0.418 1.2838 -14.5194 2.7317 24.2282 19 7.4247 1.4632 -2.0454 3.3059 1.976 2.9231 0.3124 0.893 1.1419 -1.2833 -0.0253 0.269 -1.5963 -1.0624 -0.3425 1.0892 -0.1515 0.1659 0.7341 0.1147 1.2284 -48.1235 16.0055 17.1522 20 7.1904 -1.0964 0.1885 8.0273 0.375 5.2873 0.2188 -0.4747 1.1962 0.2373 0.0326 -0.0248 -0.5658 -0.2377 -0.1544 0.5371 -0.0056 0.1068 0.5299 -0.1517 0.9343 -49.9155 11.1776 24.9724 21 3.1815 -3.2228 -3.7544 5.5597 5.1182 5.1818 0.0688 1.3701 0.8007 -3.5931 0.55 -0.2817 -2.3401 -0.1192 -0.6051 1.0805 -0.1082 0.067 0.7955 -0.0733 0.7229 -45.7141 3.8162 11.1429 22 4.6405 -0.7497 -0.6878 3.7187 -0.8325 2.3957 0.8977 1.0002 -1.5133 0.6213 -0.4817 -0.5401 0.3487 1.0072 -0.3955 0.8998 -0.1659 -0.5818 1.4137 -0.5519 1.8035 -17.9304 11.4571 27.3674 23 4.9426 -5.0536 2.608 5.1686 -2.8475 3.4279 0.0348 -0.0979 -0.3746 -0.6768 -0.0157 -1.9904 0.298 0.912 0.1221 0.8636 -0.1193 0.3005 1.7975 -0.7603 2.4943 -7.9521 13.1373 26.3276 24 0.6215 -1.485 0.7209 4.1738 -1.7472 0.8325 0.3352 0.0057 0.2132 -0.3451 -0.0125 -1.4797 0.0076 0.7008 -0.8536 1.2243 0.1033 -0.358 1.6898 -0.75 3.1359 -16.5732 13.7334 28.074
Refinement TLS group Show large table (6 x 24) 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 16 through 87 )A16 - 87 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 88 through 114 )A88 - 114 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 115 through 177 )A115 - 177 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 178 through 269 )A178 - 269 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 270 through 299 )A270 - 299 6 X-RAY DIFFRACTION 6 chain 'A' and (resid 300 through 341 )A300 - 341 7 X-RAY DIFFRACTION 7 chain 'B' and (resid 345 through 366 )B345 - 366 8 X-RAY DIFFRACTION 8 chain 'B' and (resid 367 through 402 )B367 - 402 9 X-RAY DIFFRACTION 9 chain 'B' and (resid 403 through 407 )B403 - 407 10 X-RAY DIFFRACTION 10 chain 'B' and (resid 408 through 476 )B408 - 476 11 X-RAY DIFFRACTION 11 chain 'B' and (resid 477 through 489 )B477 - 489 12 X-RAY DIFFRACTION 12 chain 'B' and (resid 490 through 498 )B490 - 498 13 X-RAY DIFFRACTION 13 chain 'B' and (resid 499 through 511 )B