Software | Name | Version | Classification | NB |
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DENZO | | data reduction | SCALEPACK | | data scaling | PHASER | | phasing | RESOLVE | | phasing | PHENIX | 1.4_4refinement | PDB_EXTRACT | 3.006 | data extraction | HKL-2000 | | data reduction | HKL-2000 | | data scaling | | | | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QA1 Resolution: 2.89→29.68 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.57 / Phase error: 34.85 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.273 | 2422 | 5.11 % |
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Rwork | 0.235 | - | - |
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obs | 0.237 | 47393 | 95.4 % |
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.51 Å2 / ksol: 0.25 e/Å3 |
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Displacement parameters | Biso mean: 119.11 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 13.914 Å2 | -0 Å2 | -22.214 Å2 |
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2- | - | -12.814 Å2 | 0 Å2 |
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3- | - | - | -1.1 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.89→29.68 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 10174 | 0 | 167 | 18 | 10359 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.005 | 10597 | X-RAY DIFFRACTION | f_angle_d0.993 | 14559 | X-RAY DIFFRACTION | f_dihedral_angle_d15.513 | 3648 | X-RAY DIFFRACTION | f_chiral_restr0.072 | 1683 | X-RAY DIFFRACTION | f_plane_restr0.008 | 1910 | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | Number | Refine-ID | Type | Rms dev position (Å) |
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1 | 1 | A3159 | X-RAY DIFFRACTION | POSITIONAL | 1 | 2 | B3159 | X-RAY DIFFRACTION | POSITIONAL0.049 | 1 | 3 | C3230 | X-RAY DIFFRACTION | POSITIONAL0.033 | | | | | | |
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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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2.89-2.946 | 0.434 | 117 | 0.425 | 2121 | X-RAY DIFFRACTION | 78 | 2.946-3.01 | 0.426 | 138 | 0.407 | 2545 | X-RAY DIFFRACTION | 92 | 3.01-3.08 | 0.452 | 137 | 0.386 | 2562 | X-RAY DIFFRACTION | 92 | 3.08-3.157 | 0.451 | 141 | 0.369 | 2562 | X-RAY DIFFRACTION | 93 | 3.157-3.242 | 0.375 | 144 | 0.336 | 2573 | X-RAY DIFFRACTION | 94 | 3.242-3.338 | 0.351 | 141 | 0.294 | 2662 | X-RAY DIFFRACTION | 95 | 3.338-3.445 | 0.299 | 123 | 0.277 | 2691 | X-RAY DIFFRACTION | 97 | 3.445-3.568 | 0.309 | 133 | 0.241 | 2692 | X-RAY DIFFRACTION | 97 | 3.568-3.711 | 0.286 | 135 | 0.236 | 2698 | X-RAY DIFFRACTION | 97 | 3.711-3.879 | 0.273 | 136 | 0.221 | 2681 | X-RAY DIFFRACTION | 98 | 3.879-4.083 | 0.248 | 157 | 0.209 | 2712 | X-RAY DIFFRACTION | 98 | 4.083-4.338 | 0.229 | 149 | 0.187 | 2720 | X-RAY DIFFRACTION | 98 | 4.338-4.672 | 0.21 | 156 | 0.186 | 2717 | X-RAY DIFFRACTION | 98 | 4.672-5.14 | 0.24 | 165 | 0.183 | 2746 | X-RAY DIFFRACTION | 99 | 5.14-5.879 | 0.265 | 137 | 0.213 | 2757 | X-RAY DIFFRACTION | 99 | 5.879-7.388 | 0.292 | 149 | 0.217 | 2770 | X-RAY DIFFRACTION | 99 | 7.388-29.684 | 0.205 | 164 | 0.197 | 2762 | X-RAY DIFFRACTION | 97 |
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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 | 1.3811 | -1.1742 | 0.1419 | 1.2356 | -0.1892 | -0.0935 | -0.4036 | 0.2776 | 0.1616 | 0.4841 | 0.6847 | 0.3891 | -0.4294 | 0.2059 | -0.1237 | 0.8991 | 0.3975 | 0.6333 | 0.6312 | -0.1763 | 0.601 | 27.8732 | -20.7386 | 40.6726 | 2 | 0.6769 | -0.1755 | -0.118 | 0.5763 | -0.222 | 0.435 | 0.2931 | 0.4372 | -0.3719 | 0.3274 | -0.0144 | 0.6017 | -0.0658 | -0.1535 | 0.1138 | -0.8469 | -0.004 | 0.3256 | 0.3708 | -0.0637 | 0.4868 | 32.0911 | -29.1434 | 18.9003 | 3 | 1.4903 | -0.535 | -0.3607 | 0.3855 | -0.2086 | 0.0276 | -0.7046 | 0.232 | 0.232 | 0.6423 | 0.1821 | 0.015 | -1.454 | -0.0816 | -1.5909 | 0.4103 | 0.664 | 0.6844 | 0.0803 | -0.2486 | -0.0205 | 27.2344 | -14.4308 | 36.9179 | 4 | -1.618 | -0.4093 | 0.1682 | 1.2287 | -0.5877 | 1.7246 | 0.2013 | -0.7105 | -0.5352 | -0.128 | 0.9151 | 0.9267 | 0.7221 | -0.7317 | -0.9434 | 0.421 | 0.1073 | -0.1368 | 0.7326 | 0.3207 | 1.4487 | 16.404 | -15.3177 | 4.9732 | 5 | -1.5516 | -0.3255 | 0.7032 | 0.8483 | -0.8287 | 0.6214 | 0.0877 | -0.1769 | -0.3708 | 0.0529 | 0.3771 | 0.8692 | 0.0736 | -0.4995 | -0.7386 | 0.1322 | 0.9545 | -0.196 | 0.4599 | 0.4555 | 1.2337 | 14.2653 | -9.2309 | 9.548 | 6 | 1.0581 | -0.3355 | -0.5271 | 2.4601 | -0.4053 | 2.1812 | -0.1929 | 0.0933 | 0.2173 | 0.6495 | -0.0892 | 0.0293 | -0.8361 | -0.267 | -0.0296 | 0.4046 | 0.0795 | 0.1745 | 0.3182 | -0.059 | 0.4217 | 38.3754 | -15.2521 | 32.1727 | 7 | 0.4347 | -0.3628 | -0.0197 | 0.186 | 0.0127 | -0.0321 | 0.0262 | 0.3786 | 0.1174 | -0.1299 | -0.1527 | -0.1875 | -0.0488 | 0.1717 | -0.2367 | -1.3262 | 0.5114 | 0.9539 | 0.3223 | -0.2593 | -0.0179 | 39.1519 | -15.51 | 5.5351 | 8 | 0.3802 | -0.4968 | -0.9839 | -0.2219 | -1.6572 | 1.1883 | 0.1023 | 0.2416 | 0.394 | -0.1863 | -0.5953 | 0.2591 | -0.5082 | 0.2656 | 0.0594 | 0.8286 | -0.1598 | -0.2191 | 0.4313 | -0.0831 | 0.4753 | 50.3793 | -29.1995 | 26.7673 | 9 | 0.5382 | -0.2311 | -0.3487 | 1.2965 | -0.3964 | 1.9217 | -0.0378 | -0.3105 | -0.109 | -0.0936 | -0.4543 | -0.0141 | -0.5815 | 0.3167 | 0.2053 | 0.7661 | -0.3014 | -0.2452 | 0.7004 | 0.0985 | 0.627 | 52.8273 | -35.3131 | 36.927 | 10 | 0.4144 | 0.177 | 0.3893 | 0.7888 | 0.5989 | -0.4819 | 0.4414 | 0.1609 | 0.0533 | 0.0324 | -0.4508 | -0.221 | 0.7023 | -0.1015 | -0.1195 | 2.0625 | 0.3624 | -0.2436 | 1.2491 | -0.2356 | 0.5874 | 52.7866 | -84.4193 | 27.27 | 11 | 0.3252 | 0.2468 | 0.3892 | 0.8845 | 0.703 | -0.6317 | 0.3802 | -0.188 | 0.2012 | 0.1683 | -0.6018 | 0.125 | 1.2467 | -0.0067 | 0.0259 | 2.1892 | -0.2256 | -0.3375 | 0.8182 | -0.0545 | 0.761 | 44.1967 | -76.588 | 47.6692 | 12 | 0.3656 | 0.3002 | 0.1226 | 0.3122 | 0.7387 | 0.1144 | 0.5834 | 0.2693 | -0.57 | 0.3013 | -0.3196 | -0.0384 | 1.0001 | -0.2066 | -0.1631 | 2.3659 | 0.1521 | -0.3574 | 0.7137 | -0.2007 | 0.7716 | 54.892 | -89.8452 | 31.3649 | 13 | -0.1519 | 0.5259 | 0.3006 | 1.8922 | 1.6785 | 1.2662 | 0.2548 | -0.3313 | 0.009 | 0.3084 | 0.2751 | -0.0849 | 1.3903 | -0.5279 | -0.4443 | 2.7933 | -0.7742 | -0.4309 | 0.9249 | 0.108 | 0.8988 | 38.2994 | -97.773 | 59.1297 | 14 | 0.0907 | 0.2226 | 0.2333 | 1.5466 | 1.4691 | 1.6654 | 0.2846 | 0.3088 | -0.411 | 0.4162 | 0.4788 | -0.0448 | 1.6251 | 0.0657 | -0.5312 | 2.8912 | -0.6615 | -0.5545 | 0.7017 | 0.0724 | 0.9777 | 41.2864 | -103.1859 | 53.5399 | 15 | 0.8005 | 0.0373 | 0.3865 | 0.8362 | 0.181 | 1.4108 | 0.3678 | 0.0953 | -0.1696 | 0.6214 | 0.0898 | -0.535 | 1.7765 | -0.1886 | -0.2148 | 2.0511 | 0.3518 | -0.4577 | 0.8044 | -0.1075 | 0.7751 | 61.3021 | -82.899 | 38.8287 | 16 | 0.3412 | 0.1522 | 0.4674 | 0.6267 | 0.5924 | -0.3728 | 0.3487 | -0.0559 | -0.064 | 0.5453 | 0.0879 | 0.1876 | 1.3259 | -0.2114 | -0.1205 | 2.1876 | -0.1124 | -0.4013 | 0.7234 | -0.0501 | 0.6559 | 53.3344 | -83.6384 | 64.4596 | 17 | 1.2749 | 1.3076 | 0.6132 | 0.5084 | 0.1945 | 5.0545 | -0.1102 | 0.2578 | 0.1382 | 0.6998 | -0.0117 | -0.158 | 1.0482 | 0.972 | 0.0084 | 1.1049 | 0.0087 | -0.244 | 1.0154 | 0.1921 | 0.8104 | 60.8421 | -64.777 | 45.3384 | 18 | -0.1056 | 0.4516 | -0.2773 | 0.5288 | -0.0439 | 3.4416 | -0.3665 | 0.0946 | 0.3003 | -0.1575 | 0.123 | 0.3246 | 0.3171 | 0.5388 | 0.1582 | 0.7237 | 0.026 | 0.0196 | 0.9241 | 0.1576 | 0.7984 | 61.5573 | -57.8939 | 35.0493 | 19 | 0.6811 | 0.0812 | -0.2309 | 2.2942 | -0.0683 | 0.4468 | 1.1735 | 0.129 | 0.1728 | 1.1021 | -0.3209 | 0.0444 | 0.0561 | -0.0439 | 0.1361 | 1.029 | -0.2847 | 0.3153 | 0.9078 | -0.2389 | 0.4475 | 16.9738 | -61.0954 | 34.1518 | 20 | 1.2185 | -0.7774 | -0.4475 | 3.0114 | -0.2975 | 0.2131 | 0.463 | 0.1994 | -0.0393 | -0.6742 | -0.2798 | 0.547 | 0.2887 | -0.2996 | 0.0399 | 0.155 | -0.1627 | 0.0198 | 0.5265 | -0.3704 | 0.8184 | 10.9109 | -65.8631 | 11.0679 | 21 | 0.9337 | 0.3252 | -0.5556 | 2.2677 | -0.1914 | 0.2218 | -0.026 | 0.1297 | 0.1606 | 0.641 | -0.2694 | -0.1551 | -0.0791 | 0.0267 | 0.1348 | 1.0773 | -0.2477 | 0.0238 | 0.4932 | -0.1558 | 0.5201 | 22.4127 | -58.6866 | 30.3096 | 22 | 1.537 | 0.7195 | 0.0869 | 0.7902 | 1.0264 | 1.1065 | -0.3172 | 0.4029 | 0.8853 | -1.0907 | 0.1464 | 0.8334 | -0.4923 | -0.5997 | 0.1151 | 1.1403 | -0.0721 | -0.363 | 0.8312 | 0.0424 | 1.2529 | 19.6782 | -46.1608 | -0.7432 | 23 | 1.2747 | 0.9776 | 0.1746 | 0.731 | 0.7009 | 0.497 | -0.4512 | -0.1691 | 1.4111 | -0.6495 | 0.2044 | 0.5285 | -0.5792 | 0.2722 | 0.0306 | 1.1134 | -0.2064 | -0.3577 | 0.5731 | 0.001 | 1.2498 | 25.2469 | -42.1301 | 4.8742 | 24 | 1.2074 | 0.7029 | -0.1944 | 2.2347 | -0.1966 | 0.3586 | 0.1484 | 0.0245 | 0.0645 | 0.9406 | -0.3988 | -0.21 | -0.2131 | 0.1089 | 0.2598 | 0.5888 | -0.3422 | -0.0531 | 0.441 | -0.0653 | 0.6207 | 25.2886 | -68.9502 | 24.9392 | 25 | 0.9594 | -0.9672 | -0.5579 | 0.9071 | 0.423 | 0.3704 | 0.3409 | -0.0646 | 0.1664 | -0.1775 | -0.2749 | -0.0147 | -0.3317 | 0.056 | 0.2551 | -0.3374 | 0.3145 | 0.2675 | 0.4818 | -0.24 | 0.5164 | 26.2686 | -67.6823 | -1.7094 | 26 | -0.1678 | 0.0037 | -0.8648 | 0.5298 | -0.432 | 0.055 | 0.2013 | -0.151 | -0.515 | 0.6792 | -0.0862 | -0.1564 | 1.3073 | -0.4272 | -0.0519 | 0.8167 | -0.502 | -0.1941 | 0.9203 | 0.0284 | 0.8186 | 16.4735 | -85.236 | 18.2396 | 27 | 0.1534 | 0.0287 | -0.3313 | 0.4276 | -0.3041 | 0.8445 | 0.0502 | 0.3427 | -0.2373 | 0.2781 | -0.0424 | 0.6695 | 1.3417 | -0.3354 | 0.0978 | 1.8413 | -0.7645 | 0.0154 | 1.1985 | -0.0371 | 1.0713 | 10.1501 | -90.1492 | 29.5383 | 28 | 0.0011 | 0.0591 | 0.0862 | 0.0415 | -0.0083 | -0.0745 | -0.0816 | -0.2191 | 0.1069 | 0.1388 | 0.0883 | 0.1967 | -0.107 | -0.0906 | -0.0353 | 0.0207 | 0.4834 | 0.3989 | 0.6664 | -0.2911 | 1.3715 | 25.2747 | -15.6103 | 27.8968 | 29 | -0.3716 | 0.2277 | -0.0045 | -0.1801 | 0.0708 | 0.4552 | -0.1404 | 0.0052 | -0.2076 | -0.099 | -0.2178 | 0.0024 | 0.0999 | 0.1029 | 0.0118 | 2.1301 | -0.0258 | -0.0882 | 0.6006 | 0.0487 | 0.9221 | 50.1088 | -91.0025 | 39.2839 | 30 | -0.2146 | 0.0952 | -0.0532 | 0.2301 | 0.108 | 0.0329 | 0.0298 | -0.1038 | 0.2897 | 0.545 | -0.1816 | -0.3728 | 0.0501 | 0.0201 | -0.0239 | 0.882 | -0.2822 | -0.3947 | 0.7557 | 0.1404 | 1.3587 | 21.3545 | -56.3125 | 21.5523 |
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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 13:462 | X-RAY DIFFRACTION | 2 | chain A and resid 47:1013 | X-RAY DIFFRACTION | 3 | chain A and resid 102:1874 | X-RAY DIFFRACTION | 4 | chain A and resid 188:2145 | X-RAY DIFFRACTION | 5 | chain A and resid 215:2696 | X-RAY DIFFRACTION | 6 | chain A and resid 270:3447 | X-RAY DIFFRACTION | 7 | chain A and resid 345:3878 | X-RAY DIFFRACTION | 8 | chain A and resid 388:4229 | X-RAY DIFFRACTION | 9 | chain A and resid 423:51010 | X-RAY DIFFRACTION | 10 | chain B and resid 14:4611 | X-RAY DIFFRACTION | 11 | chain B and resid 47:10112 | X-RAY DIFFRACTION | 12 | chain B and resid 102:18713 | X-RAY DIFFRACTION | 13 | chain B and resid 188:21414 | X-RAY DIFFRACTION | 14 | chain B and resid 215:26915 | X-RAY DIFFRACTION | 15 | chain B and resid 270:34416 | X-RAY DIFFRACTION | 16 | chain B and resid 345:38717 | X-RAY DIFFRACTION | 17 | chain B and resid 388:42218 | X-RAY DIFFRACTION | 18 | chain B and | | | | | | | | | | | | | | | | | |
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