Software | Name | Version | Classification |
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PHENIX | (dev_2341: ???)refinementXDS | | data reductionXSCALE | | data scalingPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JRI Resolution: 1.706→49.042 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 24.07 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1926 | 16334 | 4.93 % |
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Rwork | 0.165 | - | - |
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obs | 0.1664 | 167233 | 99.75 % |
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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: 1.706→49.042 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 9783 | 0 | 634 | 1200 | 11617 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 10656 | X-RAY DIFFRACTION | f_angle_d1.413 | 14504 | X-RAY DIFFRACTION | f_dihedral_angle_d14.086 | 5941 | X-RAY DIFFRACTION | f_chiral_restr0.197 | 1612 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1759 | | | | | |
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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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1.7055-1.7249 | 0.3639 | 526 | 0.3692 | 10120 | X-RAY DIFFRACTION | 96 | 1.7249-1.7452 | 0.3578 | 556 | 0.3389 | 10548 | X-RAY DIFFRACTION | 100 | 1.7452-1.7665 | 0.355 | 492 | 0.3291 | 10438 | X-RAY DIFFRACTION | 100 | 1.7665-1.7888 | 0.3519 | 526 | 0.3303 | 10582 | X-RAY DIFFRACTION | 100 | 1.7888-1.8124 | 0.3437 | 483 | 0.3152 | 10551 | X-RAY DIFFRACTION | 100 | 1.8124-1.8372 | 0.3248 | 587 | 0.3103 | 10509 | X-RAY DIFFRACTION | 100 | 1.8372-1.8634 | 0.3393 | 522 | 0.3096 | 10428 | X-RAY DIFFRACTION | 100 | 1.8634-1.8913 | 0.3264 | 534 | 0.2989 | 10637 | X-RAY DIFFRACTION | 100 | 1.8913-1.9208 | 0.3383 | 532 | 0.2996 | 10453 | X-RAY DIFFRACTION | 100 | 1.9208-1.9523 | 0.3298 | 477 | 0.298 | 10573 | X-RAY DIFFRACTION | 100 | 1.9523-1.986 | 0.3087 | 456 | 0.2631 | 10537 | X-RAY DIFFRACTION | 100 | 1.986-2.0221 | 0.2567 | 506 | 0.2349 | 10551 | X-RAY DIFFRACTION | 100 | 2.0221-2.061 | 0.247 | 535 | 0.2177 | 10591 | X-RAY DIFFRACTION | 100 | 2.061-2.103 | 0.255 | 548 | 0.1985 | 10465 | X-RAY DIFFRACTION | 100 | 2.103-2.1488 | 0.2119 | 581 | 0.1769 | 10472 | X-RAY DIFFRACTION | 100 | 2.1488-2.1988 | 0.2097 | 579 | 0.162 | 10468 | X-RAY DIFFRACTION | 100 | 2.1988-2.2537 | 0.2099 | 506 | 0.1629 | 10558 | X-RAY DIFFRACTION | 100 | 2.2537-2.3147 | 0.1902 | 528 | 0.1515 | 10490 | X-RAY DIFFRACTION | 100 | 2.3147-2.3828 | 0.1934 | 639 | 0.1415 | 10416 | X-RAY DIFFRACTION | 100 | 2.3828-2.4597 | 0.183 | 590 | 0.1393 | 10488 | X-RAY DIFFRACTION | 100 | 2.4597-2.5476 | 0.1771 | 540 | 0.139 | 10498 | X-RAY DIFFRACTION | 100 | 2.5476-2.6496 | 0.1863 | 590 | 0.1421 | 10502 | X-RAY DIFFRACTION | 100 | 2.6496-2.7702 | 0.1905 | 492 | 0.1474 | 10541 | X-RAY DIFFRACTION | 100 | 2.7702-2.9162 | 0.1729 | 603 | 0.1445 | 10438 | X-RAY DIFFRACTION | 100 | 2.9162-3.0989 | 0.1759 | 581 | 0.1507 | 10475 | X-RAY DIFFRACTION | 100 | 3.0989-3.3381 | 0.1699 | 520 | 0.1488 | 10550 | X-RAY DIFFRACTION | 100 | 3.3381-3.6739 | 0.1739 | 549 | 0.1395 | 10500 | X-RAY DIFFRACTION | 100 | 3.6739-4.2053 | 0.1384 | 624 | 0.1204 | 10402 | X-RAY DIFFRACTION | 100 | 4.2053-5.2972 | 0.1398 | 557 | 0.1126 | 10445 | X-RAY DIFFRACTION | 100 | 5.2972-49.0625 | 0.1673 | 575 | 0.1595 | 10464 | X-RAY DIFFRACTION | 100 |
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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 | 0.8438 | 0.0474 | 0.1573 | 0.9706 | 0.182 | 1.6213 | -0.0082 | -0.1051 | 0.1538 | 0.0164 | -0.0308 | 0.0429 | -0.2159 | -0.3009 | -0 | 0.2802 | 0.0719 | -0.011 | 0.1997 | -0.031 | 0.2443 | -12.8716 | 28.9074 | -16.4221 | 2 | 0.531 | -0.1516 | -0.091 | 0.5288 | -0.4813 | 0.5442 | 0.0584 | -0.2119 | -0.1204 | 0.2128 | 0.007 | 0.0773 | 0.2133 | -0.4019 | -0 | 0.2945 | 0.0298 | 0.0153 | 0.4295 | -0.0664 | 0.3023 | -24.5127 | 21.2136 | -5.8517 | 3 | 1.537 | 0.1202 | 0.597 | 0.2505 | 0.2252 | 0.9723 | -0.022 | -0.1375 | 0.0503 | 0.0251 | 0.0044 | -0.0563 | 0.0021 | -0.0031 | -0.0004 | 0.2701 | 0.0239 | 0.0039 | 0.1837 | -0.0086 | 0.2519 | 2.5219 | 21.5809 | -8.3469 | 4 | 0.9014 | 0.3606 | 0.2601 | 0.2752 | 0.1228 | 1.9162 | -0.0239 | 0.2484 | 0.122 | -0.1039 | 0.0138 | -0.064 | -0.2394 | 0.2704 | -0.0023 | 0.3286 | -0.0475 | 0.0228 | 0.2104 | 0.033 | 0.2664 | 10.7116 | 27.7851 | -32.7253 | 5 | 0.4254 | 0.2179 | 0.0366 | 0.4343 | 0.3574 | 0.3634 | -0.0462 | 0.4447 | -0.0214 | -0.2964 | 0.0898 | -0.2266 | 0.1087 | 0.3197 | 0.0001 | 0.4116 | -0.0294 | 0.1229 | 0.5895 | -0.0148 | 0.3868 | 21.4171 | 21.4543 | -44.1993 | 6 | 0.3014 | 0.1176 | -0.2535 | 0.6047 | 0.3277 | 0.5755 | -0.0529 | 0.3026 | 0.1309 | -0.2245 | -0.0293 | -0.0598 | -0.2107 | 0.2188 | -0.0001 | 0.3711 | -0.0388 | 0.0567 | 0.2955 | 0.0274 | 0.2773 | 4.4926 | 24.5351 | -45.2369 | 7 | 0.6252 | 0.054 | 0.0785 | 0.4652 | -0.4663 | 0.5455 | -0.047 | 0.0899 | 0.0559 | -0.1623 | -0.0691 | -0.123 | -0.3139 | -0.157 | 0.001 | 0.3942 | 0.0521 | -0.0264 | 0.3434 | -0.0099 | 0.2787 | -16.8437 | 24.9561 | -43.2255 | 8 | 0.5369 | 0.2171 | 0.2962 | 0.5617 | -0.1449 | 0.3338 | -0.0985 | 0.1508 | -0.1712 | -0.3345 | 0.0151 | 0.0085 | -0.1248 | -0.1649 | -0.0002 | 0.3497 | 0.0387 | -0.0232 | 0.3791 | -0.0365 | 0.2504 | -23.0469 | 18.2364 | -52.4658 | 9 | 1.0102 | 0.0606 | 0.4921 | 0.3108 | 0.2812 | 1.0917 | -0.0105 | 0.1213 | -0.042 | -0.1384 | 0.0166 | -0.0252 | -0.094 | 0.0476 | -0 | 0.3178 | -0.0087 | 0.0349 | 0.2072 | 0.0037 | 0.2566 | 2.3171 | 19.6473 | -35.7398 | 10 | 0.8596 | -0.1667 | 0.0046 | 0.2734 | -0.0853 | 1.1135 | 0.027 | 0.1397 | -0.1115 | 0.0004 | -0.015 | -0.0589 | 0.1557 | 0.1514 | 0 | 0.2141 | 0.0355 | 0.0009 | 0.258 | -0.0412 | 0.2564 | -22.1867 | 51.6426 | -26.24 | 11 | 0.6697 | 0.3421 | 0.0609 | 0.6845 | 0.6809 | 0.8298 | -0.0887 | 0.1966 | 0.015 | 0.0669 | 0.0667 | -0.1863 | -0.1388 | 0.2081 | -0.0001 | 0.2216 | 0.0527 | 0.0434 | 0.4217 | 0.0063 | 0.2845 | -7.3436 | 57.1219 | -35.2826 | 12 | 0.4974 | 0.1331 | -0.1922 | 0.5796 | 0.2803 | 0.33 | 0.0438 | 0.1125 | -0.1339 | 0.077 | -0.0223 | -0.0875 | 0.2021 | 0.1805 | 0 | 0.2112 | 0.0258 | 0.0038 | 0.2714 | -0.0216 | 0.2891 | -11.8358 | 53.9422 | -13.503 | 13 | 0.9075 | -0.5408 | -0.3286 | 0.9111 | 0.0516 | 1.1262 | 0.0331 | -0.1289 | 0.0758 | 0.0983 | 0.0059 | -0.1121 | -0.017 | 0.0554 | 0.0005 | 0.2412 | 0.0019 | -0.0229 | 0.2173 | -0.0121 | 0.2375 | -18.7265 | 59.5098 | 4.7144 | 14 | 0.3908 | -0.0252 | -0.234 | 0.1517 | -0.0261 | 0.2968 | -0.0217 | -0.2636 | -0.2664 | 0.1762 | 0.0758 | -0.1486 | 0.2153 | 0.0027 | 0.0069 | 0.3652 | 0.0332 | -0.0543 | 0.2843 | 0.0227 | 0.3307 | -13.662 | 48.1482 | 6.0803 | 15 | 0.2979 | -0.0216 | -0.1186 | 0.079 | -0.0406 | 0.1189 | -0.0129 | 0.1843 | 0.1581 | 0.0616 | 0.0431 | -0.1423 | -0.3034 | 0.305 | 0.0001 | 0.3029 | -0.0384 | 0.0087 | 0.348 | 0.0163 | 0.3162 | -11.6813 | 67.2119 | -20.7289 | 16 | 1.004 | 0.5144 | 0.0576 | 1.116 | 0.2149 | 0.2026 | -0.049 | 0.1797 | 0.0701 | -0.019 | 0.0051 | -0.0154 | -0.285 | 0.1406 | -0.0101 | 0.1793 | 0.0127 | 0.0277 | 0.2672 | 0.0124 | 0.2117 | -27.02 | 65.3033 | -31.8113 | 17 | 1.0373 | -0.1185 | 0.4107 | 0.5963 | 0.2032 | 1.3035 | 0.0217 | -0.0635 | -0.0612 | 0.0425 | -0.0298 | 0.0822 | 0.094 | -0.112 | 0.0001 | 0.1933 | -0.0178 | 0.0118 | 0.1962 | 0.0061 | 0.2408 | -45.6693 | 55.9697 | -12.4732 | 18 | 0.5659 | -0.3079 | -0.2339 | 0.5577 | -0.3941 | 0.7905 | -0.0387 | -0.0947 | 0.202 | -0.0618 | -0.0257 | 0.146 | -0.1447 | -0.1583 | 0 | 0.2319 | -0.0091 | 0.0262 | 0.3194 | -0.042 | 0.2845 | -58.9391 | 65.4398 | -7.0253 | 19 | 0.4302 | -0.0432 | -0.121 | 0.3885 | -0.1714 | 0.2738 | 0.0186 | 0.024 | 0.0238 | -0.0226 | -0.0637 | 0.0929 | 0.0951 | -0.191 | 0.0001 | 0.2024 | 0.0169 | 0.0145 | 0.2792 | -0.0141 | 0.2635 | -53.9108 | 60.5276 | -23.0542 | 20 | 0.7497 | 0.5518 | 0.1081 | 0.7175 | -0.1315 | 1.0746 | 0.019 | 0.1541 | 0.0043 | 0.0234 | 0.012 | 0.1219 | -0.0694 | 0.0439 | -0.0009 | 0.2445 | 0.0224 | -0.005 | 0.2756 | -0.0007 | 0.2275 | -45.4982 | 58.5869 | -43.3026 | 21 | 0.2019 | -0.2421 | -0.0252 | 0.3299 | 0.1415 | 0.3077 | 0.0562 | 0.1112 | 0.0565 | -0.1412 | -0.0187 | 0.2016 | -0.173 | 0.056 | -0.0001 | 0.2975 | 0.0179 | -0.0356 | 0.2983 | 0.0146 | 0.2657 | -51.0158 | 62.6759 | -52.0444 | 22 | 0.6 | -0.1086 | 0.1268 | 0.3805 | -0.3593 | 0.5241 | 0.0273 | 0.1038 | -0.1224 | -0.1501 | -0.0048 | 0.1218 | 0.115 | -0.1074 | -0.0001 | 0.2637 | 0.0043 | -0.0105 | 0.2735 | -0.0114 | 0.2881 | -52.9024 | 55.9951 | -38.9423 | 23 | 0.7796 | -0.391 | -0.2793 | 1.2493 | 0.0646 | 0.4077 | 0.0305 | 0.0568 | 0.1242 | -0.0626 | -0.0384 | 0.0216 | -0.297 | 0.0595 | -0.001 | 0.1977 | -0.0066 | 0.0276 | 0.1963 | -0.002 | 0.2385 | -37.7058 | 69.1772 | -11.2497 |
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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 11 through 101 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 102 through 120 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 121 through 330 )4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 10 through 101 )5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 102 through 120 )6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 121 through 147 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 148 through 188 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 189 through 222 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 223 through 330 )10 | X-RAY DIFFRACTION | 10 | chain 'C' and (resid 18 through 101 )11 | X-RAY DIFFRACTION | 11 | chain 'C' and (resid 102 through 124 )12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resid 125 through 147 )13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 148 through 222 )14 | X-RAY DIFFRACTION | 14 | chain 'C' and (resid 223 through 252 )15 | X-RAY DIFFRACTION | 15 | chain 'C' and (resid 253 through 272 )16 | X-RAY DIFFRACTION | 16 | chain 'C' | | | | | | | | | | | | | | | |
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