Software | Name | Version | Classification |
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PHENIX | (PHENIX.REFINE: 1.6.1_357)refinementMOSFLM | | data reductionSCALA | | data scalingSnB | | phasing | | | | |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.6→72.931 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 30.33 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2847 | 1262 | 10 % |
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Rwork | 0.2335 | - | - |
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obs | 0.2388 | 12614 | 97.58 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.522 Å2 / ksol: 0.369 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.3046 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -6.005 Å2 | 0 Å2 |
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3- | - | - | 4.7004 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.6→72.931 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2086 | 0 | 0 | 66 | 2152 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.008 | 2137 | X-RAY DIFFRACTION | f_angle_d1.239 | 2902 | X-RAY DIFFRACTION | f_dihedral_angle_d17.725 | 771 | X-RAY DIFFRACTION | f_chiral_restr0.082 | 319 | X-RAY DIFFRACTION | f_plane_restr0.004 | 366 | | | | | |
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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 | A782 | X-RAY DIFFRACTION | POSITIONAL | 1 | 2 | B782 | X-RAY DIFFRACTION | POSITIONAL0.241 | 2 | 1 | C89 | X-RAY DIFFRACTION | POSITIONAL | 2 | 2 | D89 | X-RAY DIFFRACTION | POSITIONAL0.196 | | | | | | | | |
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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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2.6001-2.7042 | 0.4158 | 141 | 0.3174 | 1267 | X-RAY DIFFRACTION | 100 | 2.7042-2.8272 | 0.354 | 142 | 0.2972 | 1275 | X-RAY DIFFRACTION | 99 | 2.8272-2.9763 | 0.3459 | 139 | 0.2869 | 1258 | X-RAY DIFFRACTION | 100 | 2.9763-3.1628 | 0.3364 | 141 | 0.2729 | 1275 | X-RAY DIFFRACTION | 100 | 3.1628-3.407 | 0.3169 | 140 | 0.2528 | 1255 | X-RAY DIFFRACTION | 99 | 3.407-3.7498 | 0.264 | 143 | 0.2302 | 1279 | X-RAY DIFFRACTION | 99 | 3.7498-4.2924 | 0.2742 | 140 | 0.1876 | 1264 | X-RAY DIFFRACTION | 98 | 4.2924-5.4077 | 0.1957 | 140 | 0.1705 | 1264 | X-RAY DIFFRACTION | 97 | 5.4077-72.9592 | 0.3018 | 136 | 0.2456 | 1215 | X-RAY DIFFRACTION | 88 |
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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 | 1.8331 | -0.2796 | 3.9697 | 2.9482 | -0.5451 | 8.4976 | -0.1856 | 0.2046 | -1.0936 | -0.7506 | -0.3247 | 0.0442 | -0.2097 | -1.4543 | 0.7435 | 0.4396 | 0.0793 | -0.0445 | 0.1384 | -0.104 | 0.3876 | -4.5729 | -43.517 | -0.7444 | 2 | 8.4808 | -1.3124 | -3.6641 | 0.4138 | 0.5213 | 1.7932 | -0.0049 | -0.2919 | -2.1642 | -0.0077 | -0.4915 | -0.0536 | -0.2969 | 0.5242 | 0.3347 | 0.5104 | -0.0628 | -0.0362 | 0.3198 | 0.0717 | 0.591 | -11.792 | -44.6617 | 14.8732 | 3 | 2.863 | -0.714 | 2.5189 | 3.8209 | 0.4834 | 3.6975 | 0.3341 | -0.2444 | 0.9582 | -0.3044 | -0.3087 | -1.0368 | 0.2461 | -0.3593 | -0.1182 | 0.2456 | -0.0056 | 0.021 | 0.3484 | -0.1956 | 0.5943 | 2.817 | -25.6851 | 19.8896 | 4 | 3.399 | 0.4573 | -1.3298 | 4.0965 | -0.3591 | 7.6443 | 0.1052 | -0.2897 | 0.0423 | -0.0534 | 0.2717 | 0.1401 | 0.417 | 0.4243 | -0.4175 | 0.2563 | -0.0399 | -0.0334 | 0.1742 | 0.0495 | 0.2409 | -11.0937 | -36.5628 | 15.663 | 5 | 4.4977 | -1.1697 | 0.9542 | 2.7462 | 1.3076 | 1.4845 | -0.2559 | 0.4781 | -0.8661 | 1.4467 | 0.279 | -0.3137 | 1.0955 | -0.2445 | 0.0054 | 0.4804 | 0.0058 | -0.0367 | 0.4666 | -0.043 | 0.2868 | -2.3556 | -36.7856 | 19.2284 | 6 | 2.3347 | -1.5426 | 1.2855 | 2.7841 | -2.1077 | 1.9485 | 0.037 | -0.7362 | 1.1589 | -0.6575 | -1.377 | 0.2714 | -0.1173 | 0.1674 | -0.6465 | 0.4441 | -0.2292 | 0.1346 | 0.5069 | -0.3964 | -0.0032 | -10.3542 | -21.5088 | 19.1481 | 7 | 3.176 | -0.9856 | -0.0168 | 4.0419 | 2.0881 | 3.2579 | 0.6601 | -0.7524 | 0.6525 | 0.408 | 0.5276 | -0.9835 | -0.784 | 0.4223 | -0.9002 | 0.1891 | -0.0914 | 0.0842 | 0.3301 | -0.1086 | 0.3702 | -3.3916 | -24.4893 | 18.8981 | 8 | 7.016 | -3.6768 | -2.6762 | 4.5536 | 0.1938 | 2.8838 | 0.2236 | 0.6687 | 0.4593 | -0.8712 | -0.2854 | -0.5975 | -0.3179 | -0.7086 | -0.1049 | 0.2725 | 0.01 | -0.0836 | 0.3646 | -0.054 | 0.2239 | -13.2603 | -25.6884 | 11.0533 | 9 | 5.2427 | -4.0798 | 0.5285 | 4.7907 | -3.064 | 1.9913 | 0.3109 | 0.4406 | 1.1219 | -0.7401 | -0.6889 | -1.2758 | 2.3816 | -1.3799 | 0.5203 | 0.1557 | -0.0242 | 0.204 | 0.5906 | -0.1204 | 0.5959 | -10.0155 | -3.6494 | 25.5909 | 10 | 4.3727 | 0.2196 | -4.1579 | 3.9767 | -0.654 | 5.6488 | 0.5067 | 3.2345 | -0.0132 | -0.6046 | -0.1657 | -1.1031 | 0.368 | 0.418 | -0.0855 | 0.6152 | 0.3574 | -0.0608 | 0.7113 | 0.0155 | 0.6186 | -29.1931 | -6.97 | 15.0311 | 11 | 9.7894 | -6.8401 | 0.3113 | 9.769 | 4.6183 | 6.8632 | 1.0606 | 0.9966 | 1.4577 | -4.4992 | -1.8829 | 0.6526 | -1.6734 | -0.5369 | 1.2829 | 1.0234 | 0.4202 | -0.3605 | 0.9319 | -0.1956 | 0.1175 | -29.8843 | -3.9446 | 12.7605 | 12 | 5.3854 | -3.8971 | -3.658 | 8.3027 | 6.4159 | 5.0639 | 0.5856 | -0.2413 | 1.7442 | -0.0834 | 1.3002 | -2.7089 | -0.1854 | 0.6553 | -1.9384 | 0.4415 | -0.1215 | 0.1284 | 0.5213 | -0.2333 | 0.7972 | -14.3517 | -3.5946 | 28.9943 | 13 | 2.1016 | 0.2499 | -0.8906 | 7.7556 | 1.3013 | 1.023 | 1.1195 | 0.2877 | 3.9286 | -2.454 | -0.7439 | 1.0326 | 0.8276 | -0.4149 | -0.4197 | 0.7375 | -0.0126 | 0.2193 | 0.4612 | 0.191 | 1.4414 | -18.6038 | 2.4761 | 16.0705 | 14 | 5.1882 | 2.3814 | 3.9402 | 6.3126 | 7.216 | 8.6444 | 1.2861 | 0.7356 | -0.2069 | 1.3676 | -0.4532 | -1.0853 | 1.7885 | -1.5465 | 0.7137 | 0.3562 | 0.1124 | 0.1416 | 0.4084 | -0.1021 | 0.3883 | -24.9094 | -9.6431 | 27.1241 | 15 | 8.0618 | 0.6079 | -1.9812 | 3.5572 | 0.8749 | 3.6004 | -0.052 | 1.4602 | 1.2278 | -0.1544 | -0.6962 | -0.3561 | -0.5206 | -1.2551 | 0.6722 | 0.5249 | 0.2994 | -0.0136 | 0.8619 | -0.0281 | 0.4572 | -26.3347 | -9.7116 | 20.0063 | 16 | 0.5126 | 1.5359 | 0.5377 | 3.8377 | 1.5115 | 0.5298 | 0.4257 | 0.2183 | -0.3172 | 0.6539 | -0.7185 | -0.0242 | 0.4091 | -0.1669 | 0.0185 | 0.5381 | -0.0444 | 0.1433 | 0.5998 | -0.1129 | 0.3184 | -17.0855 | -15.8407 | 24.379 | 17 | 5.6818 | -0.2202 | -1.9383 | 1.3063 | 1.8165 | 4.2018 | 0.699 | -0.2745 | 2.3812 | -0.5263 | 0.5591 | -0.4213 | 0.0547 | 0.3144 | -1.1695 | 0.361 | -0.0002 | 0.0775 | 0.3788 | -0.1116 | 0.7989 | 0.1781 | -17.296 | 21.4707 | 18 | 6.3896 | 3.8512 | 4.6697 | 9.5799 | 8.3488 | 7.73 | 0.7629 | -1.1785 | -0.0715 | 1.7965 | -2.0941 | 1.2788 | 2.8557 | -1.484 | 0.0238 | 0.4234 | 0.1707 | -0.038 | 0.5376 | -0.1169 | 0.2377 | -34.2789 | -13.8288 | 18.8035 |
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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 4:15)2 | X-RAY DIFFRACTION | 2 | (CHAIN A AND RESID 16:31)3 | X-RAY DIFFRACTION | 3 | (CHAIN A AND RESID 32:54)4 | X-RAY DIFFRACTION | 4 | (CHAIN A AND RESID 55:74)5 | X-RAY DIFFRACTION | 5 | (CHAIN A AND RESID 75:87)6 | X-RAY DIFFRACTION | 6 | (CHAIN A AND RESID 88:96)7 | X-RAY DIFFRACTION | 7 | (CHAIN A AND RESID 97:114)8 | X-RAY DIFFRACTION | 8 | (CHAIN A AND RESID 115:134)9 | X-RAY DIFFRACTION | 9 | (CHAIN B AND RESID 24:35)10 | X-RAY DIFFRACTION | 10 | (CHAIN B AND RESID 36:46)11 | X-RAY DIFFRACTION | 11 | (CHAIN B AND RESID 47:55)12 | X-RAY DIFFRACTION | 12 | (CHAIN B AND RESID 56:71)13 | X-RAY DIFFRACTION | 13 | (CHAIN B AND RESID 72:81)14 | X-RAY DIFFRACTION | 14 | (CHAIN B AND RESID 82:96)15 | X-RAY DIFFRACTION | 15 | (CHAIN B AND RESID 97:115)16 | X-RAY DIFFRACTION | 16 | (CHAIN B AND RESID 116:130)17 | X-RAY DIFFRACTION | 17 | (CHAIN C AND RESID 167:180)18 | X-RAY DIFFRACTION | 18 | (CHAIN D AND | | | | | | | | | | | | | | | | | |
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