Software | Name | Version | Classification |
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PHENIX | (dev_3092: ???)refinementXDS | | data reductionSCALA | | data scalingHKL2Map | | phasing | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.693→49.115 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.8
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2375 | 3641 | 3.51 % |
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Rwork | 0.2001 | - | - |
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obs | 0.2015 | 197326 | 99.14 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Refinement step | Cycle: LAST / Resolution: 2.693→49.115 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 24310 | 0 | 6 | 877 | 25193 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.002 | 24772 | X-RAY DIFFRACTION | f_angle_d0.517 | 33625 | X-RAY DIFFRACTION | f_dihedral_angle_d8.939 | 14413 | X-RAY DIFFRACTION | f_chiral_restr0.044 | 3910 | X-RAY DIFFRACTION | f_plane_restr0.003 | 4313 | | | | | |
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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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2.693-2.7236 | 0.3803 | 201 | 0.3498 | 5608 | X-RAY DIFFRACTION | 88 | 2.7236-2.7556 | 0.3408 | 231 | 0.312 | 6386 | X-RAY DIFFRACTION | 100 | 2.7556-2.7892 | 0.3743 | 231 | 0.3 | 6371 | X-RAY DIFFRACTION | 100 | 2.7892-2.8246 | 0.3523 | 230 | 0.2944 | 6396 | X-RAY DIFFRACTION | 99 | 2.8246-2.8617 | 0.3018 | 226 | 0.287 | 6359 | X-RAY DIFFRACTION | 100 | 2.8617-2.9009 | 0.3198 | 233 | 0.2824 | 6476 | X-RAY DIFFRACTION | 100 | 2.9009-2.9424 | 0.3536 | 230 | 0.2736 | 6279 | X-RAY DIFFRACTION | 100 | 2.9424-2.9863 | 0.3555 | 234 | 0.2784 | 6388 | X-RAY DIFFRACTION | 100 | 2.9863-3.0329 | 0.3533 | 231 | 0.275 | 6326 | X-RAY DIFFRACTION | 98 | 3.0329-3.0826 | 0.3045 | 225 | 0.2665 | 6363 | X-RAY DIFFRACTION | 99 | 3.0826-3.1358 | 0.3052 | 229 | 0.2671 | 6339 | X-RAY DIFFRACTION | 100 | 3.1358-3.1928 | 0.3055 | 238 | 0.2472 | 6432 | X-RAY DIFFRACTION | 100 | 3.1928-3.2542 | 0.2524 | 237 | 0.2285 | 6376 | X-RAY DIFFRACTION | 100 | 3.2542-3.3206 | 0.3095 | 234 | 0.2286 | 6357 | X-RAY DIFFRACTION | 100 | 3.3206-3.3928 | 0.2409 | 238 | 0.2171 | 6419 | X-RAY DIFFRACTION | 100 | 3.3928-3.4717 | 0.2223 | 237 | 0.2088 | 6407 | X-RAY DIFFRACTION | 100 | 3.4717-3.5585 | 0.2563 | 235 | 0.1984 | 6419 | X-RAY DIFFRACTION | 100 | 3.5585-3.6547 | 0.2602 | 228 | 0.1925 | 6402 | X-RAY DIFFRACTION | 100 | 3.6547-3.7622 | 0.2268 | 224 | 0.1817 | 6361 | X-RAY DIFFRACTION | 100 | 3.7622-3.8836 | 0.225 | 229 | 0.1725 | 6417 | X-RAY DIFFRACTION | 100 | 3.8836-4.0223 | 0.2067 | 236 | 0.1716 | 6397 | X-RAY DIFFRACTION | 100 | 4.0223-4.1833 | 0.204 | 232 | 0.1629 | 6344 | X-RAY DIFFRACTION | 100 | 4.1833-4.3735 | 0.1621 | 234 | 0.1423 | 6359 | X-RAY DIFFRACTION | 100 | 4.3735-4.604 | 0.1689 | 229 | 0.1373 | 6349 | X-RAY DIFFRACTION | 99 | 4.604-4.8922 | 0.1917 | 235 | 0.1346 | 6304 | X-RAY DIFFRACTION | 98 | 4.8922-5.2695 | 0.1921 | 229 | 0.153 | 6401 | X-RAY DIFFRACTION | 100 | 5.2695-5.799 | 0.1983 | 234 | 0.1708 | 6358 | X-RAY DIFFRACTION | 99 | 5.799-6.6364 | 0.1817 | 231 | 0.1668 | 6297 | X-RAY DIFFRACTION | 99 | 6.6364-8.3545 | 0.1908 | 237 | 0.1831 | 6388 | X-RAY DIFFRACTION | 100 | 8.3545-49.1235 | 0.2013 | 230 | 0.2034 | 6320 | 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 | 4.3509 | 1.0167 | 1.5395 | 4.8699 | 2.4884 | 2.4778 | -0.2277 | -0.4287 | -0.0441 | 0.7334 | 0.252 | -0.0843 | 0.0425 | -0.2296 | -0.0398 | 0.8499 | 0.093 | 0.0542 | 0.717 | -0.0212 | 0.3778 | -16.853 | 15.2999 | -43.7565 | 2 | 1.1703 | -0.0724 | 1.1452 | 0.8413 | 0.1845 | 3.7707 | -0.0648 | -0.2593 | 0.1054 | 0.2211 | 0.02 | -0.0082 | -0.2183 | -0.1186 | 0.0443 | 0.3816 | -0.0054 | 0.0189 | 0.3114 | -0.0214 | 0.3317 | -24.6592 | 19.6771 | -81.0069 | 3 | 0.1121 | -0.0409 | -0.3248 | 0.0338 | -0.1239 | 1.9182 | 0.0328 | -0.045 | -0.0293 | -0.0227 | -0.0187 | 0.0258 | -0.1252 | -0.0533 | -0.0127 | 0.3493 | -0.0042 | -0.0169 | 0.3398 | -0.0165 | 0.34 | -22.0913 | 13.4709 | -130.7518 | 4 | 0.6197 | -0.135 | 0.4744 | 1.2488 | 0.8331 | 2.5274 | -0.0448 | -0.2997 | -0.0699 | 0.4248 | -0.0218 | 0.2134 | 0.068 | -0.3282 | 0.0689 | 0.574 | -0.0057 | 0.15 | 0.6438 | 0.0496 | 0.4596 | -34.8021 | -3.9147 | -61.5801 | 5 | 0.035 | -0.1037 | 0.1059 | 0.0414 | -0.1123 | 2.1922 | 0.0496 | 0.0256 | -0.0176 | -0.0428 | -0.0281 | 0.0563 | 0.1573 | -0.0437 | -0.031 | 0.2716 | -0.0195 | 0.0091 | 0.317 | -0.0355 | 0.3644 | -30.6219 | -8.5658 | -115.7006 | 6 | 1.5157 | 0.0769 | -0.8581 | 0.9405 | 0.0316 | 3.6933 | -0.1014 | -0.3422 | -0.1215 | 0.5315 | 0.0496 | -0.0609 | 0.1799 | 0.0948 | 0.0422 | 0.6654 | 0.044 | -0.0319 | 0.4802 | 0.0336 | 0.381 | -9.3593 | -5.3345 | -57.5304 | 7 | 0.0354 | -0.0079 | 0.1026 | 0.2738 | 0.2027 | 1.5718 | 0.0298 | 0.0217 | -0.003 | 0.0539 | -0.0193 | -0.0327 | -0.0086 | 0.2474 | -0.015 | 0.2405 | 0.0045 | -0.0047 | 0.3773 | 0.0262 | 0.3268 | -6.0462 | -2.0906 | -111.79 | 8 | 5.2684 | -0.3139 | 0.4054 | 0.6625 | 0.0207 | 7.2383 | 0.6282 | -0.8306 | 0.4222 | 0.2019 | -0.2125 | 0.0647 | -1.0805 | 0.1235 | -0.3934 | 2.4383 | 0.1806 | 0.1408 | 1.4124 | 0.0422 | 0.588 | 8.5055 | 34.1964 | 16.3665 | 9 | 0.6412 | 0.0966 | 0.586 | 0.3838 | -0.0581 | 0.5922 | 0.2267 | -0.5401 | -0.0319 | 0.2894 | -0.1013 | 0.1051 | 0.0956 | -0.1778 | -0.1022 | 2.0742 | 0.1568 | 0.1942 | 1.2429 | 0.116 | 0.491 | 8.0438 | 30.3107 | -0.2718 | 10 | 0.6591 | 0.2733 | -0.2605 | 0.1573 | -0.2957 | 2.7088 | -0.0853 | -0.3965 | -0.1827 | 0.8426 | 0.1552 | 0.031 | 0.1073 | -0.1428 | -0.0657 | 1.3187 | 0.1285 | 0.032 | 0.693 | 0.1001 | 0.4736 | 16.2336 | 26.8086 | -31.417 | 11 | 0.7373 | -0.3494 | -0.395 | 2.1045 | -0.119 | 1.0099 | -0.2477 | -0.0949 | -0.0775 | 0.3178 | 0.1249 | 0.0592 | 0.0725 | 0.0019 | 0.089 | 0.3856 | 0.005 | 0.0483 | 0.3673 | 0.0287 | 0.3157 | 15.7796 | 35.6576 | -70.4184 | 12 | 2.6294 | -1.6021 | -0.5544 | 1.1936 | 0.4618 | 1.0904 | 0.0299 | 0.0463 | -0.0765 | 0.1639 | -0.0765 | 0.0158 | 0.1913 | -0.1348 | 0.0448 | 0.4094 | -0.0758 | 0.0091 | 0.3521 | 0.0093 | 0.357 | 11.8501 | 32.7933 | -88.3729 | 13 | 0.0004 | -0.0198 | -0.0124 | 0.2349 | 0.1509 | 0.0945 | -0.1122 | 0.0907 | 0.0359 | 0.227 | 0.0628 | -0.0038 | -0.155 | 0.2926 | 0.088 | 2.7126 | 0.3898 | -0.2179 | 1.3214 | 0.0352 | 0.6493 | 26.95 | 40.0097 | 17.0634 | 14 | 0.256 | 0.0047 | 0.3698 | -0.0027 | 0.0035 | 0.5604 | -0.1561 | -0.3977 | 0.1656 | 0.9545 | 0.1316 | -0.5376 | -0.3569 | 0.298 | 0.2211 | 1.7408 | 0.1352 | -0.5134 | 0.86 | -0.0635 | 0.5377 | 33.2354 | 49.0046 | -23.3825 | 15 | 1.5402 | -0.1306 | -0.919 | 0.9462 | 0.335 | 1.876 | -0.0187 | -0.0537 | 0.1342 | 0.5355 | -0.0864 | -0.3272 | -0.4699 | -0.0017 | 0.1444 | 0.8275 | 0.0783 | -0.092 | 0.4965 | 0.0242 | 0.4279 | 22.6091 | 52.0911 | -61.3894 | 16 | 3.1162 | 1.1665 | 0.9709 | 5.0162 | 0.2989 | 2.6674 | -0.1092 | -0.08 | -0.0166 | 0.0721 | 0.0254 | -0.248 | -0.0284 | 0.1526 | 0.0882 | 0.2554 | 0.0108 | 0.0188 | 0.3131 | 0.0061 | 0.2729 | 34.3446 | 43.5252 | -86.5019 | 17 | 2.1521 | 0.5734 | -1.425 | 1.0619 | 1.0303 | 4.7901 | 0.1239 | -0.5272 | -0.0444 | 0.2469 | 0.1547 | -0.1456 | 0.3451 | -0.3999 | -0.2266 | 2.3408 | 0.3546 | -0.1733 | 1.2835 | -0.0771 | 0.5866 | 13.2966 | 54.3294 | 14.9446 | 18 | 0.6938 | 0.6736 | 1.5938 | 1.4824 | 1.7376 | 3.7089 | -0.0115 | -0.2408 | 0.1268 | 0.6069 | -0.0232 | 0.2139 | -0.4337 | -0.3529 | 0.2512 | 1.9084 | 0.2656 | -0.0639 | 1.2198 | -0.0703 | 0.4676 | 7.0829 | 57.9969 | -2.6019 | 19 | 0.3374 | 0.187 | 0.1679 | 0.1401 | -0.1263 | 1.4724 | 0.0355 | -0.1755 | 0.1075 | 0.2971 | -0.0301 | 0.0905 | -0.2405 | -0.3833 | 0.0682 | 2.0429 | 0.3731 | 0.0686 | 1.0366 | -0.0577 | 0.5082 | 5.8021 | 56.7301 | -14.215 | 20 | 0.571 | 0.3984 | 0.9865 | 0.6601 | 0.2973 | 3.2618 | 0.0623 | -0.1774 | 0.0634 | 0.6292 | -0.027 | 0.1508 | -0.043 | -0.915 | -0.0609 | 1.7969 | 0.3486 | 0.1301 | 1.0315 | 0.0295 | 0.5007 | 2.2238 | 52.3488 | -20.8003 | 21 | 1.5634 | -0.8567 | -0.8768 | 1.8322 | 2.0969 | 2.4232 | -0.069 | -0.3436 | 0.1588 | 1.0038 | 0.1554 | 0.1895 | -0.6098 | -0.5038 | -0.0268 | 1.2995 | 0.3293 | 0.0912 | 0.7737 | 0.0305 | 0.4863 | 3.4768 | 54.1977 | -34.6536 | 22 | 4.0312 | -0.7524 | -3.0807 | 2.1351 | 0.5281 | 5.2205 | -0.2324 | -0.3097 | 0.0408 | 0.4737 | 0.2525 | 0.0593 | -0.2744 | -0.5708 | -0.0441 | 0.6794 | 0.11 | -0.0485 | 0.5613 | 0.0255 | 0.3538 | 6.8817 | 47.1102 | -55.1831 | 23 | 3.2728 | 0.201 | 0.6816 | 0.2358 | 0.4362 | 1.2057 | 0.0575 | -0.039 | 0.0804 | 0.1419 | -0.0581 | 0.0064 | 0.0109 | -0.1162 | -0.0031 | 0.3961 | -0.0026 | -0.01 | 0.2972 | 0.04 | 0.3399 | 13.0471 | 59.0172 | -86.683 |
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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 206 through 276 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 277 through 542 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 543 through 749 )4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 207 through 423 )5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 424 through 749 )6 | X-RAY DIFFRACTION | 6 | chain 'C' and (resid 206 through 391 )7 | X-RAY DIFFRACTION | 7 | chain 'C' and (resid 392 through 749 )8 | X-RAY DIFFRACTION | 8 | chain 'D' and (resid 206 through 252 )9 | X-RAY DIFFRACTION | 9 | chain 'D' and (resid 253 through 332 )10 | X-RAY DIFFRACTION | 10 | chain 'D' and (resid 333 through 590 )11 | X-RAY DIFFRACTION | 11 | chain 'D' and (resid 591 through 659 )12 | X-RAY DIFFRACTION | 12 | chain 'D' and (resid 660 through 749 )13 | X-RAY DIFFRACTION | 13 | chain 'E' and (resid 206 through 252 )14 | X-RAY DIFFRACTION | 14 | chain 'E' and (resid 253 through 590 )15 | X-RAY DIFFRACTION | 15 | chain 'E' and (resid 591 through 630 )16 | X-RAY DIFFRACTION | 16 | chain 'E' | | | | | | | | | | | | | | | |
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