Software | Name | Version | Classification |
---|
PHENIX | 1.7.1_743refinementREFMAC | 5.5.0109refinement | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→35.13 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU ML: 0.55 / σ(F): 2.16 / Phase error: 24.25 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.2359 | 2145 | 5.04 % |
---|
Rwork | 0.1917 | - | - |
---|
obs | 0.194 | 42538 | 97.83 % |
---|
|
---|
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.223 Å2 / ksol: 0.365 e/Å3 |
---|
Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
---|
1- | -0.2815 Å2 | -0.2009 Å2 | -0.9922 Å2 |
---|
2- | - | -0.5259 Å2 | 0.5203 Å2 |
---|
3- | - | - | 0.8075 Å2 |
---|
|
---|
Refinement step | Cycle: LAST / Resolution: 2.05→35.13 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 5150 | 0 | 66 | 223 | 5439 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
---|
X-RAY DIFFRACTION | f_bond_d0.01 | 5320 | X-RAY DIFFRACTION | f_angle_d1.195 | 7236 | X-RAY DIFFRACTION | f_dihedral_angle_d17.069 | 1940 | X-RAY DIFFRACTION | f_chiral_restr0.078 | 822 | X-RAY DIFFRACTION | f_plane_restr0.004 | 934 | | | | | |
|
---|
Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | Number | Refine-ID | Type | Rms dev position (Å) |
---|
1 | 1 | A1998 | X-RAY DIFFRACTION | POSITIONAL | 1 | 2 | C1998 | X-RAY DIFFRACTION | POSITIONAL0.055 | 2 | 1 | D573 | X-RAY DIFFRACTION | POSITIONAL | 2 | 2 | B573 | X-RAY DIFFRACTION | POSITIONAL0.118 | | | | | | | | |
|
---|
LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
---|
2.05-2.0977 | 0.303 | 140 | 0.2387 | 2655 | X-RAY DIFFRACTION | 97 | 2.0977-2.1502 | 0.2446 | 146 | 0.222 | 2634 | X-RAY DIFFRACTION | 97 | 2.1502-2.2083 | 0.2689 | 142 | 0.2045 | 2720 | X-RAY DIFFRACTION | 97 | 2.2083-2.2733 | 0.2664 | 128 | 0.2129 | 2696 | X-RAY DIFFRACTION | 97 | 2.2733-2.3466 | 0.3208 | 133 | 0.2174 | 2653 | X-RAY DIFFRACTION | 97 | 2.3466-2.4305 | 0.276 | 141 | 0.2121 | 2696 | X-RAY DIFFRACTION | 98 | 2.4305-2.5278 | 0.2692 | 131 | 0.1995 | 2729 | X-RAY DIFFRACTION | 98 | 2.5278-2.6428 | 0.2714 | 142 | 0.2168 | 2691 | X-RAY DIFFRACTION | 98 | 2.6428-2.7821 | 0.2663 | 143 | 0.2118 | 2681 | X-RAY DIFFRACTION | 98 | 2.7821-2.9563 | 0.2748 | 129 | 0.2008 | 2721 | X-RAY DIFFRACTION | 98 | 2.9563-3.1844 | 0.2419 | 147 | 0.2066 | 2724 | X-RAY DIFFRACTION | 99 | 3.1844-3.5046 | 0.2436 | 183 | 0.193 | 2646 | X-RAY DIFFRACTION | 98 | 3.5046-4.0111 | 0.2315 | 135 | 0.1819 | 2725 | X-RAY DIFFRACTION | 99 | 4.0111-5.0512 | 0.1894 | 150 | 0.1546 | 2723 | X-RAY DIFFRACTION | 99 | 5.0512-35.135 | 0.1967 | 155 | 0.1818 | 2694 | X-RAY DIFFRACTION | 98 |
|
---|
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION 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 | 0.4157 | 0.1295 | -0.2963 | 0.669 | -0.6556 | 0.7154 | 0.1169 | -0.2029 | -0.2744 | 0.1232 | -0.0874 | 0.024 | -0.1422 | 0.2355 | 0.1428 | 0.1152 | -0.0455 | -0.021 | 0.1805 | 0.0048 | 0.2008 | 1.0978 | -18.9526 | 29.6338 | 2 | 1.1017 | -0.0105 | 0.3535 | 0.2635 | 0.0427 | 0.1211 | 0.1694 | -0.2529 | 0.0393 | 0.2341 | 0.0652 | 0.0318 | -0.2254 | -0.036 | 0.0864 | 0.3941 | -0.046 | 0.0835 | 0.1793 | -0.0325 | 0.1236 | -8.252 | -9.5466 | 38.7247 | 3 | 0.0873 | -0.0404 | 0.042 | 0.0199 | -0.0192 | 0.019 | 0.1058 | -0.0394 | -0.0187 | 0.0984 | 0.0044 | -0.1447 | -0.0665 | 0.0537 | 0.143 | 0.5346 | -0.2202 | 0.122 | 0.1707 | -0.1491 | 0.3543 | 1.9188 | -4.4701 | 33.6985 | 4 | 0.7067 | 0.0474 | -1.1682 | 0.5857 | 0.1533 | 2.0081 | 0.3057 | 0.2179 | 0.4156 | -0.108 | 0.033 | 0.0009 | -0.8783 | -0.3182 | 1.1054 | 0.4807 | -0.0093 | 0.1661 | 0.0232 | 0.018 | 0.2856 | -5.5477 | -4.9626 | 21.5637 | 5 | 0.1688 | 0.0845 | -0.0748 | 0.0707 | 0.0089 | 0.0996 | -0.0697 | 0.015 | -0.069 | 0.1466 | 0.1022 | 0.3022 | -0.2036 | -0.3743 | 0.1505 | 0.2969 | 0.2177 | 0.1345 | 0.4102 | 0.0351 | 0.2959 | -24.539 | -13.2025 | 28.8479 | 6 | 0.2725 | -0.4611 | 0.0645 | 0.9982 | 0.2156 | 0.4968 | -0.2292 | 0.1304 | -0.073 | 0.0561 | 0.09 | -0.0423 | 0.1049 | -0.0888 | -0.0443 | 0.1191 | -0.1062 | 0.0163 | 0.2133 | -0.0187 | 0.2462 | -16.4158 | -26.3979 | 24.4331 | 7 | 0.1892 | 0.0746 | -0.338 | 0.0568 | -0.1868 | 0.7735 | 0.2939 | 0.06 | 0.4406 | 0.2137 | 0.0029 | 0.0258 | -0.7116 | -0.235 | 0.3159 | 0.433 | 0.1409 | 0.1268 | 0.1012 | 0.0305 | 0.1741 | -10.358 | -6.5522 | 23.1677 | 8 | 0.3651 | -0.0469 | 0.337 | 0.4446 | 0.188 | 0.9754 | 0.1807 | 0.2449 | 0.2213 | -0.0997 | 0.0136 | -0.0254 | -0.2105 | -0.0495 | 0.6176 | 0.4007 | 0.1279 | 0.1419 | 0.2787 | 0.0814 | 0.1463 | -6.3014 | -7.2325 | 9.0713 | 9 | 0.0144 | 0.0107 | 0.0096 | 0.0117 | -0.0229 | 0.1049 | 0.0282 | 0.3576 | -0.1051 | -0.1737 | -0.0731 | -0.0371 | 0.1487 | -0.0913 | 0.0011 | 0.1726 | 0.03 | 0.0306 | 0.2044 | -0.0229 | 0.1608 | -1.2845 | -20.2821 | 16.0073 | 10 | 0.4621 | -0.0911 | 0.1171 | 0.1226 | 0.1936 | 0.4724 | 0.0176 | -0.2345 | 0.1814 | 0.1092 | -0.011 | 0.1021 | 0.1639 | -0.2147 | -0.112 | 0.0928 | -0.0291 | 0.0021 | 0.2464 | -0.0261 | 0.1369 | -12.1471 | -22.5048 | -2.3899 | 11 | 0.7552 | 0.2693 | 0.0444 | 0.3419 | 0.096 | 0.0274 | 0.0912 | -0.1591 | -0.0548 | -0.0387 | -0.1257 | -0.0216 | 0.4326 | 0.2572 | -0.0085 | 0.4743 | 0.0294 | -0.0061 | 0.2828 | 0.0666 | 0.1544 | -2.6555 | -34.8833 | 1.5412 | 12 | 0.3577 | -0.0861 | -0.0668 | 0.0828 | -0.1294 | 0.3548 | 0.0901 | -0.1244 | -0.1159 | 0.0553 | -0.1947 | 0.177 | 0.3978 | -0.1272 | -0.0138 | 0.7024 | -0.1759 | 0.0387 | 0.291 | -0.0066 | 0.3446 | -12.77 | -37.3101 | -5.2453 | 13 | 0.211 | -0.2243 | 0.4827 | 1.3833 | -0.3177 | 1.1343 | -0.0533 | 0.1295 | -0.0543 | -0.411 | -0.1197 | -0.033 | 0.6809 | -0.0492 | -0.2942 | 0.3767 | -0.026 | -0.0196 | 0.0898 | -0.0464 | 0.1121 | -5.3567 | -31.3197 | -15.8463 | 14 | 0.4279 | -0.1163 | 0.1562 | 0.0616 | -0.0347 | 0.0581 | -0.1 | -0.0626 | 0.0836 | 0.0386 | -0.0364 | -0.1047 | 0.0786 | 0.225 | -0.4245 | 0.2171 | 0.3326 | -0.0707 | 0.5224 | 0.0762 | 0.1446 | 13.5646 | -26.948 | -5.595 | 15 | 0.4949 | -0.2341 | -0.2869 | 0.4608 | 0.1445 | 0.166 | -0.169 | -0.1099 | 0.1301 | 0.1077 | -0.0866 | 0.032 | -0.1255 | 0.0725 | -0.1939 | 0.1745 | -0.0707 | -0.0669 | 0.3455 | -0.0437 | 0.1924 | 5.0701 | -13.5786 | -3.2796 | 16 | -0.0011 | -0.0003 | -0.0005 | 0.0095 | 0.0031 | 0.0004 | 0.0389 | -0.0125 | -0.0498 | -0.0647 | -0.0507 | -0.0424 | 0.1221 | 0.0618 | 0.0563 | 0.6382 | 0.3222 | 0.0345 | 0.379 | 0.1793 | 0.2354 | 5.553 | -34.5364 | -3.014 | 17 | 0.9188 | -0.2269 | 0.2321 | 0.6925 | 0.2629 | 0.2209 | 0.0098 | 0.2102 | -0.0494 | -0.346 | -0.0376 | -0.0246 | 0.3827 | 0.0038 | -0.0843 | 0.3401 | 0.0378 | -0.0282 | 0.1866 | -0.0406 | 0.0703 | -3.462 | -27.3602 | -22.9736 | 18 | 0.0127 | 0.0029 | -0.0083 | 0.0592 | -0.0306 | 0.0872 | 0.0124 | 0.177 | 0.1499 | -0.1195 | -0.0754 | 0.1539 | 0.0255 | -0.1341 | 0.0126 | 0.1468 | 0.0163 | -0.0417 | 0.1963 | 0.0066 | 0.1571 | -4.6262 | -18.3543 | -18.349 | 19 | 0.155 | -0.1154 | 0.1611 | 0.0856 | -0.1194 | 0.1697 | 0.0738 | 0.141 | 0.105 | -0.0684 | -0.0565 | 0.0451 | -0.0539 | -0.1121 | 0.1102 | 0.1344 | 0.0702 | -0.0484 | 0.3147 | -0.0078 | 0.1992 | -15.6286 | -15.7286 | -14.9139 | 20 | 0.0081 | 0.0004 | -0.0018 | 0.0002 | 0.0001 | 0.0004 | 0.0487 | -0.079 | 0.1892 | 0.1349 | -0.0718 | -0.0634 | 0.0126 | 0.1117 | 0.0004 | 0.2423 | -0.0522 | -0.0242 | 0.7632 | -0.1046 | 0.3966 | 24.5228 | -9.5817 | 5.8993 | 21 | 0.0147 | -0.0027 | 0.0008 | 0.0131 | -0.0078 | 0.0065 | 0.0063 | 0.0153 | -0.0139 | 0.0273 | 0.0276 | 0.0074 | -0.0382 | 0.0202 | -0.0005 | 0.7522 | 0.1082 | -0.2512 | 0.9676 | 0.0472 | 0.6454 | 30.9485 | -16.2186 | 4.5734 | 22 | 0.1362 | -0.0283 | 0.1365 | 0.1352 | -0.0012 | 0.1443 | 0.0773 | 0.2811 | -0.0379 | -0.063 | -0.0776 | 0.0369 | 0.015 | 0.0413 | -0.0311 | 0.1532 | -0.0751 | -0.0535 | 0.6681 | -0.0066 | 0.3314 | 29.1652 | -12.1121 | -5.9627 | 23 | 0.1239 | 0.0599 | 0.0363 | 0.0367 | -0.0011 | 0.0519 | -0.0096 | 0.1277 | -0.0791 | -0.0305 | -0.0166 | 0.0258 | 0.0128 | -0.0065 | 0.0867 | 0.1441 | -0.0591 | 0.0005 | 0.6406 | -0.1126 | 0.5074 | 15.0208 | -8.3052 | -0.6831 | 24 | 0.117 | 0.0069 | 0.0493 | 0.0114 | -0.0111 | 0.0381 | -0.1086 | -0.0164 | 0.0347 | -0.0661 | -0.1459 | 0.0657 | -0.0275 | -0.013 | -0.0022 | 0.5845 | -0.045 | -0.0684 | 0.5079 | 0.0815 | 0.5124 | 19.0947 | -2.6889 | -8.9287 | 25 | 0.0121 | -0.0264 | 0.0062 | 0.0579 | -0.0024 | 0.2224 | -0.0035 | -0.0622 | -0.003 | -0.0083 | 0.0025 | -0.0389 | -0.1296 | -0.0402 | -0.0044 | 0.3253 | -0.0601 | 0.1187 | 0.4821 | -0.1346 | 1.0417 | 23.4689 | 0.3074 | 0.3905 | 26 | 0.0798 | 0.0049 | 0.2447 | 0.0001 | 0.0135 | 0.7511 | -0.2263 | -0.0266 | -0.2144 | 0.1001 | -0.0112 | 0.0971 | -0.0979 | -0.051 | -0.0587 | 0.3232 | -0.0177 | 0.1051 | 0.5045 | 0.2318 | 0.7802 | -37.2916 | -31.7384 | 32.4262 | 27 | 0.0198 | -0.0042 | -0.0075 | 0.0078 | 0.0103 | 0.0122 | 0.0744 | 0.1641 | -0.1323 | -0.0651 | -0.0685 | 0.0225 | 0.0637 | -0.0015 | -0 | 0.1995 | -0.0924 | 0.0185 | 0.5688 | -0.0316 | 0.4062 | -40.2771 | -26.6928 | 21.9875 | 28 | 0.0378 | -0.0454 | 0.0032 | 0.0756 | -0.0331 | 0.0397 | -0.0194 | 0.0845 | -0.0918 | 0.0233 | -0.0054 | -0.0198 | -0.0239 | -0.0365 | -0.0033 | 0.1655 | -0.0895 | 0.0467 | 0.3808 | -0.045 | 0.5562 | -27.2168 | -29.8074 | 26.1684 | 29 | 0.0005 | -0.0071 | 0.0047 | 0.194 | -0.1389 | 0.0996 | -0.1295 | -0.0212 | -0.0804 | -0.0612 | -0.0277 | -0.0947 | 0.0888 | 0.0856 | -0.0353 | 0.3415 | -0.0101 | 0.0797 | 0.7685 | -0.3933 | 0.7184 | -27.4924 | -35.8139 | 18.8193 | 30 | 0.0481 | 0.0841 | 0.0095 | 0.1485 | 0.0254 | 0.0531 | -0.0294 | 0.0087 | -0.0416 | -0.0181 | -0.0084 | -0.0428 | 0.0602 | -0.0197 | -0.1211 | 0.3859 | -0.1236 | 0.0985 | 0.2775 | -0.2122 | 0.9322 | -34.4353 | -40.5054 | 23.405 |
|
---|
Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
---|
1 | X-RAY DIFFRACTION | 1 | ( CHAIN A AND RESID 3:45 )A3 - 45 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN A AND RESID 46:60 )A46 - 60 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN A AND RESID 61:75 )A61 - 75 | 4 | X-RAY DIFFRACTION | 4 | ( CHAIN A AND RESID 76:121 )A76 - 121 | 5 | X-RAY DIFFRACTION | 5 | ( CHAIN A AND RESID 122:148 )A122 - 148 | 6 | X-RAY DIFFRACTION | 6 | ( CHAIN A AND RESID 149:166 )A149 - 166 | 7 | X-RAY DIFFRACTION | 7 | ( CHAIN A AND RESID 167:211 )A167 - 211 | 8 | X-RAY DIFFRACTION | 8 | ( CHAIN A AND RESID 212:230 )A212 - 230 | 9 | X-RAY DIFFRACTION | 9 | ( CHAIN A AND RESID 231:257 )A231 - 257 | 10 | X-RAY DIFFRACTION | 10 | ( CHAIN C AND RESID 3:45 )C3 - 45 | 11 | X-RAY DIFFRACTION | 11 | ( CHAIN C AND RESID 46:60 )C46 - 60 | 12 | X-RAY DIFFRACTION | 12 | ( CHAIN C AND RESID 61:75 )C61 - 75 | 13 | X-RAY DIFFRACTION | 13 | ( CHAIN C AND RESID 76:121 )C76 - 121 | 14 | X-RAY DIFFRACTION | 14 | ( CHAIN C AND RESID 122:148 )C122 - 148 | 15 | X-RAY DIFFRACTION | 15 | ( CHAIN C AND | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|