Software | Name | Version | Classification |
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PHENIX | (phenix.refine: 1.9_1692)refinementHKL-3000 | | data reductionHKL-3000 | | data scalingPHENIX | (phenix.phaser)phasingPHENIX | (phenix.autobuild)model building Coot | | model building | | | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QQ1 Resolution: 1.8→24.774 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 21.04 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1989 | 1916 | 2.18 % | Random selection |
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Rwork | 0.1637 | - | - | - |
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obs | 0.1644 | 87879 | 90.63 % | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Refinement step | Cycle: LAST / Resolution: 1.8→24.774 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 8190 | 0 | 0 | 1157 | 9347 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.005 | 8438 | X-RAY DIFFRACTION | f_angle_d0.972 | 11422 | X-RAY DIFFRACTION | f_dihedral_angle_d12.458 | 3322 | X-RAY DIFFRACTION | f_chiral_restr0.037 | 1323 | X-RAY DIFFRACTION | f_plane_restr0.006 | 1470 | | | | | |
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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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1.8003-1.8453 | 0.2817 | 127 | 0.2461 | 5186 | X-RAY DIFFRACTION | 77 | 1.8453-1.8952 | 0.3108 | 120 | 0.2256 | 5510 | X-RAY DIFFRACTION | 81 | 1.8952-1.9509 | 0.2549 | 124 | 0.2089 | 5797 | X-RAY DIFFRACTION | 85 | 1.9509-2.0139 | 0.2576 | 125 | 0.1992 | 5801 | X-RAY DIFFRACTION | 87 | 2.0139-2.0858 | 0.216 | 131 | 0.1822 | 6037 | X-RAY DIFFRACTION | 89 | 2.0858-2.1693 | 0.21 | 142 | 0.1775 | 6121 | X-RAY DIFFRACTION | 90 | 2.1693-2.2679 | 0.2133 | 140 | 0.1678 | 6213 | X-RAY DIFFRACTION | 91 | 2.2679-2.3874 | 0.1845 | 139 | 0.1699 | 6239 | X-RAY DIFFRACTION | 93 | 2.3874-2.5369 | 0.2227 | 141 | 0.1802 | 6365 | X-RAY DIFFRACTION | 93 | 2.5369-2.7325 | 0.2273 | 138 | 0.1783 | 6413 | X-RAY DIFFRACTION | 95 | 2.7325-3.0071 | 0.2102 | 146 | 0.1805 | 6489 | X-RAY DIFFRACTION | 96 | 3.0071-3.4412 | 0.225 | 141 | 0.1668 | 6513 | X-RAY DIFFRACTION | 97 | 3.4412-4.3318 | 0.1638 | 156 | 0.1412 | 6603 | X-RAY DIFFRACTION | 98 | 4.3318-24.7766 | 0.1605 | 146 | 0.1361 | 6676 | X-RAY DIFFRACTION | 98 |
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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 | 4.9304 | -1.7313 | 0.0102 | 3.05 | -2.202 | 4.1992 | 0.0756 | -0.0553 | -0.0989 | 0.2542 | -0.057 | -0.0239 | -0.1607 | -0.4985 | -0.0304 | 0.1297 | 0.0591 | 0.0315 | 0.2774 | 0.0371 | 0.1739 | -55.7167 | 58.0774 | 25.6353 | 2 | 6.7963 | 4.9398 | 2.3006 | 7.6078 | 3.6148 | 6.0798 | 0.0126 | 0.247 | 0.7205 | -0.5279 | -0.0661 | 0.6604 | -0.7858 | -0.3135 | 0.0728 | 0.2409 | 0.075 | 0.0185 | 0.2733 | 0.0294 | 0.2824 | -54.7533 | 63.118 | 18.6569 | 3 | 3.2377 | 3.5647 | 3.5986 | 5.8419 | 3.0804 | 7.1004 | 0.0266 | -0.4558 | 0.3089 | 0.4256 | -0.1492 | 0.4133 | -0.4764 | -0.386 | 0.2367 | 0.3027 | 0.066 | 0.067 | 0.3629 | 0.0105 | 0.2833 | -50.8388 | 62.9457 | 35.2364 | 4 | 3.0524 | 1.398 | -0.3304 | 1.8295 | 0.1262 | 1.3022 | -0.0528 | 0.0662 | -0.037 | -0.0385 | 0.0991 | 0.0004 | -0.0415 | -0.0469 | -0.0453 | 0.2039 | 0.0105 | -0.0119 | 0.2225 | 0.0269 | 0.2256 | -41.1694 | 59.1674 | 24.2578 | 5 | 2.8341 | -4.1109 | -0.5491 | 7.5722 | -1.3623 | 4.9391 | 0.0065 | 0.2861 | -0.722 | -0.8141 | -0.0258 | 0.2223 | 0.5828 | 0.0699 | -0.0668 | 0.3086 | -0.0103 | -0.0066 | 0.3247 | -0.0676 | 0.4071 | -49.1418 | 46.022 | 13.1215 | 6 | 5.6293 | -1.5425 | 0.2604 | 7.5002 | -2.4183 | 7.2601 | -0.1017 | 0.0667 | 0.5791 | 0.1801 | -0.1496 | -0.6235 | -0.281 | 0.7028 | 0.3068 | 0.2254 | -0.1237 | 0.0137 | 0.2791 | -0.0417 | 0.27 | -12.0615 | 77.815 | 27.31 | 7 | 5.5299 | -6.3459 | 6.8494 | 7.3235 | -7.8135 | 8.5274 | -0.9846 | -0.6513 | -0.3056 | 2.5076 | 0.0116 | -1.5878 | -0.1004 | 1.7932 | 0.9045 | 0.7857 | 0.0449 | -0.0653 | 0.9498 | 0.1005 | 0.7657 | 2.1718 | 67.1567 | 23.6246 | 8 | 2.829 | -1.0568 | -0.1739 | 4.3953 | -1.7864 | 6.5318 | -0.0725 | -0.1367 | 0.4037 | 0.1342 | 0.0136 | -0.6734 | -0.3285 | 0.5572 | 0.059 | 0.1929 | -0.0705 | -0.02 | 0.2414 | -0.0372 | 0.3356 | -12.1565 | 75.2842 | 29.0505 | 9 | 3.5071 | -2.3542 | 0.1442 | 6.2729 | 1.2474 | 1.1806 | 0.0565 | 0.0137 | -0.09 | -0.112 | -0.0507 | -0.0916 | -0.0505 | 0.0268 | -0.0083 | 0.1576 | -0.0082 | 0.0088 | 0.1541 | 0.0163 | 0.155 | -19.3027 | 62.495 | 26.1943 | 10 | 2.447 | -0.6468 | -0.3335 | 4.775 | 0.2266 | 5.3049 | 0.1305 | 0.497 | 0.3298 | -0.6468 | -0.1013 | -0.047 | -0.2268 | -0.1576 | -0.0192 | 0.2612 | -0.0307 | -0.0094 | 0.2109 | 0.0527 | 0.1941 | -22.2055 | 75.86 | 17.3086 | 11 | 9.569 | -3.0225 | -6.4656 | 3.3593 | 1.5805 | 8.4038 | -0.57 | -0.2993 | -0.9425 | 0.292 | 0.229 | -0.3418 | 0.489 | 0.4391 | 0.4372 | 0.3195 | 0.0691 | 0.037 | 0.2283 | -0.0191 | 0.6859 | -12.8809 | 33.2301 | 26.6797 | 12 | 5.9536 | 4.4721 | -0.9285 | 6.0792 | -2.3352 | 1.3933 | 0.5565 | -1.1808 | 1.5463 | -0.2895 | 0.3968 | -0.5937 | 0.2586 | -0.7284 | -1.1247 | 0.8751 | 0.3329 | 0.0139 | 1.4457 | 0.1716 | 1.5092 | -35.5937 | 25.8528 | 27.9321 | 13 | 5.6562 | 2.6248 | -1.5881 | 3.572 | -1.1717 | 5.3235 | -0.3165 | 0.1288 | -1.0696 | 0.0677 | 0.1345 | 0.2575 | 0.6337 | -0.0948 | 0.1832 | 0.3762 | 0.0127 | 0.1074 | 0.2273 | -0.0977 | 0.7024 | -19.4114 | 30.7109 | 23.5776 | 14 | 5.6719 | -0.5254 | 0.6731 | 2.4824 | -0.6936 | 1.9501 | -0.0795 | -0.2136 | -0.5426 | 0.153 | 0.1039 | 0.1409 | 0.1322 | 0.0194 | -0.0353 | 0.197 | 0.0311 | 0.0282 | 0.1893 | 0.0054 | 0.2794 | -25.4404 | 43.378 | 29.7526 | 15 | 3.6216 | -0.4948 | 0.2448 | 3.3983 | 0.9271 | 4.4455 | -0.0333 | 0.9176 | -0.5847 | -0.4343 | 0.0156 | -0.0725 | 0.1723 | 0.1623 | 0.0251 | 0.2468 | 0.0314 | 0.0333 | 0.3117 | -0.1008 | 0.3061 | -15.1757 | 41.4824 | 17.9057 | 16 | 3.3196 | 1.52 | 1.7828 | 7.6811 | -0.316 | 7.6496 | -0.3697 | -0.3486 | 0.3295 | 0.2776 | 0.2728 | 0.991 | -0.1341 | -1.2281 | 0.058 | 0.2376 | -0.0887 | -0.0428 | 0.4298 | 0.0307 | 0.4199 | -71.3641 | 30.0803 | 60.8523 | 17 | 2.2643 | -1.0099 | -1.4035 | 5.6859 | 2.6818 | 3.3675 | -0.0213 | -0.1395 | -0.3214 | 0.2394 | -0.1169 | 0.6073 | 0.1948 | -0.7711 | 0.202 | 0.2571 | -0.0533 | -0.0451 | 0.3513 | 0.0631 | 0.3337 | -67.4067 | 29.3892 | 65.4479 | 18 | 2.2694 | -1.1526 | -0.2 | 6.195 | -1.1724 | 0.9638 | 0.0601 | 0.0248 | 0.0071 | -0.0974 | -0.0638 | 0.038 | 0.0781 | -0.0677 | 0.0115 | 0.2006 | -0.0226 | -0.037 | 0.2143 | -0.0164 | 0.1824 | -61.3071 | 42.9204 | 61.416 | 19 | 2.7935 | -0.49 | -0.0601 | 4.7591 | -0.0582 | 3.0689 | 0.0558 | 0.1958 | -0.2271 | -0.4693 | 0.0198 | 0.1263 | 0.1537 | -0.15 | -0.0867 | 0.2243 | -0.0458 | -0.0201 | 0.1912 | 0.0055 | 0.2064 | -59.1071 | 32.2412 | 57.4169 | 20 | 3.2699 | 1.5197 | 3.9862 | 2.4364 | -0.2546 | 8.368 | -0.4353 | 1.9079 | -0.846 | -0.7673 | 0.3887 | -0.6847 | 0.5455 | 1.2029 | -0.0216 | 0.6777 | -0.001 | 0.1083 | 0.5819 | -0.1115 | 0.4936 | -51.1216 | 25.9677 | 48.5937 | 21 | 7.8154 | -0.1437 | 0.8929 | 5.8413 | 0.0933 | 6.2971 | -0.1592 | -0.1358 | 0.9642 | 0.1235 | -0.025 | -0.1479 | -0.4869 | 0.048 | 0.2585 | 0.2638 | 0.0382 | 0.0095 | 0.1368 | 0.019 | 0.2349 | -61.7146 | 72.7477 | 63.3876 | 22 | 7.8787 | 7.2746 | 4.988 | 6.7059 | 4.5925 | 3.1651 | 0.5383 | 1.1374 | 2.6052 | -0.9311 | 0.3286 | -0.4318 | -1.3741 | -0.4736 | -0.8617 | 1.0355 | -0.0732 | 0.1416 | 0.9616 | 0.4595 | 1.2903 | -45.9319 | 81.8464 | 59.6837 | 23 | 4.9104 | -0.1828 | 2.6615 | 2.6661 | -0.7021 | 7.1445 | -0.1322 | -0.197 | 0.5893 | 0.1435 | -0.0313 | -0.0582 | -0.4399 | -0.0168 | 0.1621 | 0.2562 | 0.0348 | -0.0123 | 0.168 | -0.0579 | 0.3163 | -59.1533 | 72.023 | 64.8322 | 24 | 4.5702 | -0.8515 | -0.5116 | 1.522 | 0.6206 | 0.9677 | 0.1249 | 0.1286 | 0.1894 | -0.126 | -0.0693 | -0.0029 | -0.0134 | -0.0387 | -0.0517 | 0.2258 | 0.0239 | -0.019 | 0.2107 | 0.0029 | 0.1825 | -56.1722 | 61.0312 | 60.196 | 25 | 2.5399 | 2.2947 | -1.0348 | 3.5573 | -2.8747 | 3.0023 | -0.2561 | 0.5101 | 0.1303 | -0.9693 | 0.3393 | 0.4155 | 0.6873 | -0.5761 | -0.0923 | 0.4557 | -0.0267 | -0.0797 | 0.3819 | -0.0072 | 0.3241 | -70.8947 | 61.4752 | 48.3613 | 26 | 2.7791 | -0.9017 | -0.0954 | 9.0035 | 0.1109 | 6.4444 | -0.0647 | -0.6423 | -1.2929 | 0.0565 | -0.4245 | -1.1409 | 0.7649 | 0.7086 | 0.0344 | 0.2687 | 0.0802 | 0.0495 | 0.3787 | 0.0456 | 0.877 | -25.5528 | 42.6233 | 63.1589 | 27 | 3.7682 | 1.5976 | -1.725 | 4.2114 | 0.3772 | 4.772 | 0.0745 | -0.4304 | -1.1617 | 0.3045 | -0.223 | -1.2789 | 0.3258 | 0.4845 | 0.1072 | 0.2514 | 0.0322 | -0.0572 | 0.3115 | 0.0503 | 0.6905 | -27.757 | 43.7189 | 65.6045 | 28 | 3.5266 | 2.8136 | 1.3215 | 7.0173 | 0.9287 | 1.9036 | -0.0072 | 0.0076 | -0.3654 | -0.1305 | 0.1318 | -0.3038 | 0.2001 | 0.0685 | -0.0783 | 0.158 | 0.0068 | 0.0149 | 0.2125 | 0.021 | 0.2357 | -43.7479 | 41.8413 | 61.2921 | 29 | 3.4744 | 1.5351 | -0.8857 | 4.5813 | 0.2213 | 2.6977 | -0.2385 | 0.2593 | -0.3795 | -0.5622 | 0.2154 | -0.6986 | 0.1195 | 0.167 | -0.014 | 0.2274 | -0.025 | 0.0682 | 0.2279 | -0.0483 | 0.3089 | -32.3578 | 50.5964 | 57.0849 | 30 | 4.7197 | -4.5728 | 0.4457 | 4.8631 | -1.0786 | 3.5172 | -0.0689 | 1.0522 | 1.1292 | -1.9808 | 0.2731 | -0.8937 | -2.1404 | -0.1816 | -0.2008 | 0.7576 | -0.0845 | 0.0384 | 0.4366 | 0.0383 | 0.5019 | -33.9594 | 63.2537 | 51.2377 |
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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 -1:19) | 2 | X-RAY DIFFRACTION | 2 | (chain A and resid 20:40)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 41:66)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 67:162)5 | X-RAY DIFFRACTION | 5 | (chain A and resid 163:176)6 | X-RAY DIFFRACTION | 6 | (chain B and resid -1:15) | 7 | X-RAY DIFFRACTION | 7 | (chain B and resid 16:23)8 | X-RAY DIFFRACTION | 8 | (chain B and resid 24:73)9 | X-RAY DIFFRACTION | 9 | (chain B and resid 74:131)10 | X-RAY DIFFRACTION | 10 | (chain B and resid 132:176)11 | X-RAY DIFFRACTION | 11 | (chain C and resid -1:12) | 12 | X-RAY DIFFRACTION | 12 | (chain C and resid 13:22)13 | X-RAY DIFFRACTION | 13 | (chain C and resid 23:49)14 | X-RAY DIFFRACTION | 14 | (chain C and resid 50:130)15 | X-RAY DIFFRACTION | 15 | (chain C and resid 131:175)16 | X-RAY DIFFRACTION | 16 | (chain D and resid -1:28) | 17 | X-RAY DIFFRACTION | 17 | (chain D and resid 29:66)18 | X-RAY DIFFRACTION | 18 | (chain D and resid 67:116)19 | X-RAY DIFFRACTION | 19 | (chain D and resid 117:166)20 | X-RAY DIFFRACTION | 20 | (chain D and resid 167:176)21 | X-RAY DIFFRACTION | 21 | (chain E and resid -1:15) | 22 | X-RAY DIFFRACTION | 22 | (chain E and resid 18:22)23 | X-RAY DIFFRACTION | 23 | (chain E and | | | | | | | | | | | | | | | | | |
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