Software | Name | Version | Classification |
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PHENIX | (dev_5243: ???)refinementAimless | | data scalingXDS | | data reductionPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→45.16 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.96 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2032 | 2435 | 5.01 % |
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Rwork | 0.164 | - | - |
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obs | 0.166 | 48574 | 96.5 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Refinement step | Cycle: LAST / Resolution: 1.55→45.16 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3125 | 0 | 49 | 326 | 3500 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 3296 | X-RAY DIFFRACTION | f_angle_d1.024 | 4493 | X-RAY DIFFRACTION | f_dihedral_angle_d13.837 | 1218 | X-RAY DIFFRACTION | f_chiral_restr0.059 | 503 | X-RAY DIFFRACTION | f_plane_restr0.011 | 580 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.55-1.58 | 0.3273 | 144 | 0.2805 | 2621 | X-RAY DIFFRACTION | 95 | 1.58-1.62 | 0.2937 | 129 | 0.2564 | 2705 | X-RAY DIFFRACTION | 95 | 1.62-1.65 | 0.2843 | 162 | 0.222 | 2637 | X-RAY DIFFRACTION | 96 | 1.65-1.69 | 0.2322 | 122 | 0.2027 | 2710 | X-RAY DIFFRACTION | 96 | 1.7-1.74 | 0.2487 | 142 | 0.1915 | 2668 | X-RAY DIFFRACTION | 96 | 1.74-1.79 | 0.2297 | 180 | 0.1817 | 2678 | X-RAY DIFFRACTION | 96 | 1.79-1.85 | 0.2136 | 140 | 0.1704 | 2705 | X-RAY DIFFRACTION | 96 | 1.85-1.92 | 0.189 | 154 | 0.1589 | 2676 | X-RAY DIFFRACTION | 96 | 1.92-1.99 | 0.2023 | 142 | 0.1569 | 2722 | X-RAY DIFFRACTION | 97 | 1.99-2.08 | 0.172 | 124 | 0.1447 | 2731 | X-RAY DIFFRACTION | 97 | 2.08-2.19 | 0.2051 | 100 | 0.1393 | 2740 | X-RAY DIFFRACTION | 97 | 2.19-2.33 | 0.1886 | 135 | 0.1481 | 2735 | X-RAY DIFFRACTION | 97 | 2.33-2.51 | 0.2002 | 127 | 0.1524 | 2778 | X-RAY DIFFRACTION | 98 | 2.51-2.76 | 0.1976 | 139 | 0.1606 | 2765 | X-RAY DIFFRACTION | 98 | 2.76-3.16 | 0.1872 | 138 | 0.1655 | 2756 | X-RAY DIFFRACTION | 97 | 3.16-3.98 | 0.1867 | 200 | 0.1543 | 2669 | X-RAY DIFFRACTION | 97 | 3.98-45.16 | 0.2022 | 157 | 0.1609 | 2843 | X-RAY DIFFRACTION | 99 |
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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) |
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1 | 0.0553 | 0.0627 | 0.0054 | 0.1605 | 0.0943 | 0.1306 | -0.0944 | 0.1417 | -0.0565 | 0.0098 | 0.1173 | -0.0272 | 0.1152 | -0.0408 | -0.0021 | 0.1897 | -0.0577 | 0.0045 | 0.2446 | -0.0112 | 0.1546 | -1.6739 | 16.8398 | 7.206 | 2 | 0.1823 | 0.1543 | 0.0162 | 0.1716 | 0.091 | 0.0306 | 0.0905 | -0.0094 | 0.1358 | -0.0536 | 0.1663 | -0.1226 | -0.1985 | 0.097 | 0.0032 | 0.1727 | -0.0196 | 0.0075 | 0.199 | -0.0046 | 0.1612 | 7.1087 | 13.938 | -3.819 | 3 | 0.7867 | -1.1188 | -0.6262 | 1.6113 | 0.8572 | 0.7683 | 0.166 | -0.01 | 0.1507 | -0.1049 | 0.0062 | -0.1426 | 0.2411 | -0.0093 | 0.252 | 0.1676 | -0.0176 | -0.0262 | 0.1897 | 0.0328 | 0.1336 | -0.8615 | 10.2613 | 14.9118 | 4 | 0.0608 | -0.234 | -0.1046 | 0.0772 | -0.0395 | 0.1579 | 0.0079 | 0.069 | -0.0163 | -0.036 | -0.0261 | -0.0192 | -0.0155 | 0.018 | 0 | 0.1363 | -0.0006 | -0.0051 | 0.1369 | -0.0014 | 0.1464 | -10.3541 | 10.9749 | -20.2906 | 5 | 0.1076 | 0.0004 | 0.0555 | 0.1877 | -0.0845 | 0.099 | 0.0589 | 0.1968 | 0.1829 | -0.1579 | -0.0501 | -0.2795 | -0.0586 | 0.3446 | -0.0002 | 0.1677 | 0.0021 | 0.0009 | 0.2102 | 0.0084 | 0.2227 | -10.0704 | 25.1748 | -20.5934 | 6 | 0.1388 | -0.1303 | 0.1709 | 0.1777 | 0.0527 | 0.138 | -0.0334 | -0.0634 | 0.0186 | 0.0039 | 0.0259 | 0.0029 | -0.0367 | -0.0437 | 0.0003 | 0.1193 | -0.0019 | -0.0065 | 0.1248 | 0.0131 | 0.1265 | -15.0497 | 18.8681 | -14.1156 | 7 | -0.0009 | 0.003 | -0.0035 | 0.0261 | 0.047 | 0.0122 | -0.0984 | 0.3475 | 0.2612 | -0.2883 | 0.0034 | -0.2096 | -0.0013 | -0.1433 | 0.0004 | 0.3036 | 0.0177 | 0.0083 | 0.2584 | 0.0047 | 0.2281 | -17.4243 | 19.558 | -32.448 | 8 | 0.5455 | 0.1295 | 0.1812 | 0.6285 | -0.4024 | 0.3337 | 0.0291 | -0.0127 | -0.1274 | 0.0106 | 0.0252 | 0.1904 | 0.0917 | -0.0662 | 0.0017 | 0.1239 | 0.0052 | -0.0093 | 0.1484 | 0.003 | 0.1367 | -24.4058 | 10.8342 | -20.2544 | 9 | 0.0726 | 0.0856 | 0.0046 | 0.254 | 0.0569 | 0.437 | 0.0197 | -0.1117 | 0.0853 | 0.1027 | 0.0011 | 0.0573 | 0.2588 | 0.0121 | 0.019 | 0.1257 | 0.0124 | -0.0211 | 0.1537 | -0.0171 | 0.1435 | 2.5252 | 1.6481 | -29.3929 | 10 | 0.3116 | -0.3167 | -0.0765 | 0.2918 | 0.3298 | 0.3842 | -0.0822 | -0.0004 | -0.0323 | 0.0587 | 0.1458 | -0.0859 | -0.2361 | 0.1459 | 0.0138 | 0.1648 | -0.0131 | -0.0202 | 0.1934 | 0.0115 | 0.1711 | 4.6496 | 6.7378 | -25.1234 | 11 | 0.1299 | 0.0875 | -0.0083 | 0.1993 | -0.0811 | 0.1521 | -0.0338 | -0.0064 | -0.0167 | -0.0161 | 0.018 | 0.0209 | 0.0562 | 0.0001 | -0.0001 | 0.1505 | -0.0004 | -0.0131 | 0.146 | 0.0048 | 0.1449 | -11.606 | 2.7813 | -4.2265 | 12 | 0.1205 | -0.0778 | -0.1803 | 0.0519 | 0.0914 | 0.201 | 0.0006 | -0.0098 | -0.0584 | -0.0675 | 0.0708 | -0.1309 | 0.0642 | 0.0593 | -0.0002 | 0.1359 | -0.0036 | -0.0166 | 0.1312 | -0.006 | 0.166 | -7.4941 | 13.6637 | 1.7528 | 13 | 0.0201 | -0.0041 | -0.0352 | 0.0337 | 0.0316 | 0.2049 | -0.0194 | -0.0874 | 0.1154 | 0.226 | -0.0134 | -0.0746 | 0.2746 | -0.1423 | 0.0007 | 0.1742 | 0.0457 | -0.0104 | 0.1695 | -0.0074 | 0.1921 | -4.0982 | -6.3791 | -4.9473 | 14 | 0.2687 | -0.1975 | -0.4591 | 0.2262 | 0.3583 | 0.8267 | -0.2241 | -0.236 | 0.0757 | 0.1904 | 0.1346 | -0.011 | 0.4971 | 0.3145 | -0.0113 | 0.2364 | 0.0465 | -0.0018 | 0.1777 | -0.0069 | 0.1597 | -10.2695 | -7.702 | 0.9159 | 15 | 0.1822 | -0.0957 | -0.2745 | 0.231 | 0.144 | 0.2413 | -0.0735 | 0.0829 | -0.07 | 0.026 | 0.0458 | -0.0196 | 0.1698 | -0.0428 | 0.0004 | 0.1632 | -0.0032 | -0.0019 | 0.1374 | 0.0098 | 0.1369 | -13.9863 | -2.1046 | -8.1805 | 16 | 0.4474 | 0.1044 | -0.1748 | 1.1475 | -0.3181 | 0.5914 | -0.0061 | -0.0621 | -0.0086 | 0.0264 | 0.0498 | 0.0205 | -0.0021 | 0.0274 | -0 | 0.1163 | -0.0035 | -0.0031 | 0.1441 | 0.0102 | 0.1432 | -20.723 | 3.6442 | 1.0103 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 7 through 23 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 24 through 38 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 39 through 48 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 49 through 94 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 95 through 117 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 118 through 147 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 148 through 166 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 167 through 210 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 10 through 23 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 24 through 48 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 49 through 78 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 79 through 94 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 95 through 104 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 105 through 117 )15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid 118 through 147 )16 | X-RAY DIFFRACTION | 16 | chain 'B' | | | | | | | | | | | | | | | |
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