Software | Name | Version | Classification |
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BSS | | data collectionPHASER | | phasingPHENIX | (phenix.refine: 1.7.3_928)refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40.81 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9019 / SU ML: 0.17 / σ(F): 1.97 / Phase error: 17.06 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1932 | 2133 | 5.1 % |
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Rwork | 0.1532 | - | - |
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obs | 0.1552 | 41783 | 99.85 % |
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.589 Å2 / ksol: 0.38 e/Å3 |
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Displacement parameters | Biso max: 86.65 Å2 / Biso mean: 23.8799 Å2 / Biso min: 5.78 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -3.0332 Å2 | -0 Å2 | 0 Å2 |
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2- | - | -3.0332 Å2 | -0 Å2 |
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3- | - | - | 6.0664 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.8→40.81 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2911 | 0 | 18 | 367 | 3296 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.014 | 3168 | X-RAY DIFFRACTION | f_angle_d1.469 | 4313 | X-RAY DIFFRACTION | f_dihedral_angle_d15.835 | 1190 | X-RAY DIFFRACTION | f_chiral_restr0.12 | 460 | X-RAY DIFFRACTION | f_plane_restr0.008 | 564 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.7997-1.8415 | 0.2317 | 142 | 0.1931 | 2594 | 2736 | 99 | 1.8415-1.8876 | 0.2217 | 136 | 0.1754 | 2674 | 2810 | 100 | 1.8876-1.9386 | 0.2127 | 140 | 0.1635 | 2619 | 2759 | 100 | 1.9386-1.9957 | 0.19 | 155 | 0.1564 | 2609 | 2764 | 100 | 1.9957-2.0601 | 0.1851 | 163 | 0.1569 | 2616 | 2779 | 100 | 2.0601-2.1337 | 0.1935 | 123 | 0.1548 | 2660 | 2783 | 100 | 2.1337-2.2191 | 0.1732 | 137 | 0.1468 | 2646 | 2783 | 100 | 2.2191-2.3201 | 0.1937 | 139 | 0.1391 | 2646 | 2785 | 100 | 2.3201-2.4424 | 0.1847 | 140 | 0.1461 | 2625 | 2765 | 100 | 2.4424-2.5954 | 0.193 | 124 | 0.1576 | 2650 | 2774 | 100 | 2.5954-2.7958 | 0.2394 | 159 | 0.1676 | 2654 | 2813 | 100 | 2.7958-3.077 | 0.2044 | 160 | 0.1714 | 2613 | 2773 | 100 | 3.077-3.5221 | 0.1926 | 127 | 0.1495 | 2692 | 2819 | 100 | 3.5221-4.4366 | 0.169 | 137 | 0.1349 | 2671 | 2808 | 100 | 4.4366-40.8219 | 0.1853 | 151 | 0.1505 | 2681 | 2832 | 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 | 6.5929 | -4.3319 | -3.294 | 3.5767 | 3.5209 | 4.6795 | 0.0638 | -0.0063 | -0.4913 | -0.0282 | -0.3331 | 1.5122 | 0.6969 | -0.8447 | 0.3648 | 0.4049 | -0.1057 | 0.0192 | 0.3423 | -0.0067 | 0.7302 | 20.9848 | -2.7332 | 27.0392 | 2 | 1.0691 | 0.2629 | 0.1825 | 5.0088 | -0.5115 | 1.5055 | -0.0148 | 0.2013 | -0.012 | -0.8839 | 0.0381 | 0.1468 | 0.1215 | 0.0299 | -0.0345 | 0.2023 | -0.0027 | 0.0039 | 0.1486 | -0.0031 | 0.0815 | 29.7092 | 10.0816 | 16.7937 | 3 | 1.9444 | -1.2563 | -1.5521 | 3.9023 | 1.4178 | 1.5165 | -0.0314 | 0.0024 | -0.0166 | -0.1141 | 0.0226 | -0.1459 | 0.0054 | 0.0313 | 0.0449 | 0.0779 | 0.0134 | -0.001 | 0.0764 | 0.0334 | 0.058 | 35.488 | 13.0569 | 27.4562 | 4 | 3.7552 | -1.9333 | -2.5763 | 8.0722 | 5.3336 | 4.2828 | 0.0777 | 0.2226 | 0.3033 | -0.4471 | 0.2109 | -0.6713 | -0.0233 | 0.0775 | -0.2875 | 0.099 | 0.0033 | 0.0153 | 0.1215 | 0.0068 | 0.1795 | 46.3747 | 11.6415 | 22.7139 | 5 | 1.9823 | -1.0705 | -0.2633 | 2.5725 | 0.5628 | 0.5123 | -0.0156 | 0.1024 | 0.1096 | -0.3007 | -0.0102 | -0.1714 | 0.0389 | 0.0216 | 0.0278 | 0.1134 | 0.0123 | 0.0156 | 0.0949 | 0.0201 | 0.0511 | 33.6139 | 18.9801 | 23.8451 | 6 | 4.6053 | 0.4824 | 0.5533 | 2.7875 | -1.2487 | 7.7179 | -0.1593 | -0.1169 | 0.129 | -0.2592 | 0.2653 | -0.582 | -0.2668 | 0.6799 | -0.0536 | 0.059 | -0.0385 | 0.0184 | 0.0718 | -0.0069 | 0.2334 | 42.4432 | 25.4764 | 27.7361 | 7 | 2.4505 | -0.5583 | -0.8044 | 3.4759 | 1.5277 | 1.87 | -0.1267 | -0.0201 | 0.0059 | 0.0185 | 0.062 | 0.1241 | 0.2179 | -0.0155 | 0.0664 | 0.1076 | 0.0018 | -0.0132 | 0.0799 | 0.0279 | 0.0529 | 28.0547 | 9.0076 | 27.3443 | 8 | 4.9749 | 4.1939 | 2.8696 | 7.3673 | 5.1087 | 7.1821 | 0.167 | -0.2194 | 0.1185 | 0.6776 | -0.1093 | -0.1714 | 0.4258 | -0.1828 | -0.0231 | 0.1545 | 0.0165 | -0.0218 | 0.0817 | 0.0224 | 0.0932 | 37.0609 | 2.8959 | 31.4584 | 9 | 3.2976 | 0.1088 | -0.622 | 4.4299 | 5.5244 | 8.2375 | -0.0706 | 0.0842 | -0.0017 | 0.519 | 0.6357 | -0.787 | 0.7486 | 1.1147 | -0.4151 | 0.2165 | 0.0874 | -0.015 | 0.1874 | 0.0082 | 0.1961 | 46.036 | -1.5295 | 23.2179 | 10 | 4.6248 | -3.5436 | 2.754 | 8.077 | -1.9464 | 7.2428 | 0.0939 | 0.972 | -0.0478 | -1.0722 | -0.4341 | -1.7677 | -0.3765 | 0.595 | 0.3292 | 0.3263 | 0.0441 | 0.1079 | 0.4015 | 0.0271 | 0.4232 | 43.3368 | -24.0659 | 22.5936 | 11 | 4.7382 | 4.9425 | 4.4581 | 5.1768 | 4.7153 | 4.4718 | 0.3777 | 0.0843 | 0.5982 | -0.2949 | -0.6582 | 0.633 | -0.7058 | -0.2832 | 0.4024 | 0.3694 | 0.0635 | 0.0136 | 0.2903 | -0.0437 | 0.4128 | 22.5089 | 1.3235 | 36.0036 | 12 | 1.8118 | -1.0058 | -0.3411 | 6.9098 | -1.2516 | 2.1161 | 0.0771 | -0.1123 | 0.0929 | 0.6314 | -0.0151 | -0.062 | -0.1527 | -0.0013 | -0.0762 | 0.0772 | -0.011 | -0.0306 | 0.1037 | -0.0046 | 0.0773 | 28.048 | -12.56 | 42.841 | 13 | 1.0177 | 0.6624 | 0.3568 | 3.9914 | 1.7784 | 0.8361 | 0.092 | -0.1905 | -0.1102 | 0.6925 | -0.0826 | 0.4173 | 0.1611 | 0.0436 | -0.0044 | 0.2008 | -0.0278 | -0.0083 | 0.1577 | 0.0316 | 0.0812 | 29.3127 | -18.1362 | 47.3277 | 14 | 2.0739 | 2.3116 | 2.4092 | 5.5042 | 3.5729 | 3.2141 | 0.0303 | 0.0335 | -0.0465 | -0.0414 | 0.0588 | -0.2129 | 0.026 | 0.063 | -0.0487 | 0.0693 | -0.0036 | 0.0109 | 0.09 | 0.0402 | 0.0628 | 34.0442 | -16.6652 | 33.7028 | 15 | 3.2335 | 2.2743 | 3.3704 | 4.1015 | 4.9996 | 6.4074 | 0.0647 | 0.0503 | -0.41 | 0.0541 | 0.2016 | -0.5054 | 0.0346 | 0.2548 | -0.2404 | 0.0913 | 0.001 | 0.0285 | 0.1515 | 0.0197 | 0.2562 | 45.0674 | -16.3778 | 38.5377 | 16 | 1.7082 | 2.0221 | 0.4147 | 4.3974 | 1.12 | 0.3159 | 0.1157 | -0.1309 | -0.1222 | 0.3066 | -0.072 | -0.1223 | 0.129 | -0.0408 | -0.0565 | 0.1033 | -0.0144 | -0.0156 | 0.0994 | 0.0228 | 0.0584 | 31.9337 | -21.8376 | 37.8036 | 17 | 5.2385 | -0.2776 | 0.1494 | 3.5365 | -0.9513 | 7.7883 | 0.0326 | 0.1907 | -0.2311 | 0.1818 | 0.2044 | -0.7222 | 0.6496 | 0.5604 | -0.1128 | 0.1084 | 0.0398 | -0.0054 | 0.0792 | 0.007 | 0.2345 | 39.572 | -29.7974 | 33.5294 | 18 | 4.152 | -0.1863 | 0.3669 | 4.1634 | -0.0931 | 4.19 | -0.0108 | 0.1521 | 0.0909 | -0.1532 | -0.0097 | 0.2136 | -0.1585 | -0.2429 | 0.0252 | 0.0852 | -0.0034 | 0.0008 | 0.0582 | 0.0082 | 0.0756 | 24.0529 | -14.6488 | 31.3235 | 19 | 5.6637 | -1.4027 | -1.4208 | 5.5394 | 0.5579 | 7.7706 | -0.1297 | -0.364 | 0.2242 | 0.0033 | 0.2592 | -0.1099 | -0.3165 | 0.3838 | -0.078 | 0.1145 | -0.0168 | -0.0275 | 0.0586 | 0.0345 | 0.078 | 34.8086 | -4.7244 | 40.0599 | 20 | 4.5545 | -0.5719 | -0.2171 | 8.3779 | 5.537 | 4.8772 | -0.0172 | 0.2897 | -0.3604 | -0.7478 | 0.1515 | -0.4691 | -0.2212 | 0.1566 | -0.1305 | 0.2047 | -0.0179 | 0.0488 | 0.1087 | 0.0283 | 0.1775 | 36.5956 | -6.746 | 29.6978 | 21 | 4.8537 | -0.4667 | -1.3766 | 7.4668 | 4.807 | 7.54 | -0.3809 | 0.0994 | -0.223 | -0.4156 | 0.3322 | -0.4204 | -0.2144 | 0.4957 | 0.0705 | 0.1475 | -0.0473 | 0.0301 | 0.1306 | 0.0505 | 0.2457 | 46.2444 | -3.2624 | 37.8851 | 22 | 2.4287 | 1.5215 | -2.8237 | 0.9941 | -1.6978 | 3.8129 | 0.0923 | -0.4509 | 0.509 | 0.2525 | -0.2283 | -0.6409 | 0.1763 | -0.177 | 0.0919 | 0.1449 | -0.0472 | -0.067 | 0.2664 | -0.0724 | 0.3376 | 44.3798 | 21.7905 | 39.0485 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resseq 74:83)A74 - 83 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 84:109)A84 - 109 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 110:128)A110 - 128 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resseq 129:144)A129 - 144 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resseq 145:163)A145 - 163 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resseq 164:177)A164 - 177 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resseq 178:213)A178 - 213 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resseq 214:224)A214 - 224 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resseq 225:244)A225 - 244 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resseq 245:255)A245 - 255 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resseq 75:84)B75 - 84 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resseq 85:99)B85 - 99 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resseq 100:109)B100 - 109 | 14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resseq 110:128)B110 - 128 | 15 | X-RAY DIFFRACTION | 15 | chain 'B' and ( | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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