Software | Name | Version | Classification |
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HKL-3000 | | data collectionSHELXS | | phasingPHENIX | (phenix.refine: 1.8.1_1168)refinementHKL-3000 | | data reductionHKL-3000 | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→41.265 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 29.42 / Stereochemistry target values: MLHL
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2862 | 1079 | 5.14 % | random |
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Rwork | 0.2392 | - | - | - |
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obs | 0.2415 | 21008 | 99.59 % | - |
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all | - | 21029 | - | - |
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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: 3→41.265 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 6932 | 0 | 54 | 0 | 6986 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 7134 | X-RAY DIFFRACTION | f_angle_d1.011 | 9618 | X-RAY DIFFRACTION | f_dihedral_angle_d16.293 | 2693 | X-RAY DIFFRACTION | f_chiral_restr0.075 | 1038 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1243 | | | | | |
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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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3-3.1356 | 0.3465 | 135 | 0.3027 | 2485 | X-RAY DIFFRACTION | 99 | 3.1356-3.3009 | 0.3137 | 125 | 0.2942 | 2468 | X-RAY DIFFRACTION | 100 | 3.3009-3.5076 | 0.3089 | 137 | 0.2799 | 2442 | X-RAY DIFFRACTION | 100 | 3.5076-3.7783 | 0.2849 | 144 | 0.2547 | 2477 | X-RAY DIFFRACTION | 100 | 3.7783-4.1582 | 0.2807 | 140 | 0.2355 | 2480 | X-RAY DIFFRACTION | 100 | 4.1582-4.7591 | 0.254 | 112 | 0.2165 | 2511 | X-RAY DIFFRACTION | 100 | 4.7591-5.993 | 0.2693 | 139 | 0.2412 | 2518 | X-RAY DIFFRACTION | 100 | 5.993-41.2687 | 0.2954 | 147 | 0.2175 | 2548 | 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 | 3.099 | 2.1004 | -0.7462 | 5.5297 | 3.3174 | 3.8851 | -0.2165 | 0.824 | 0.2328 | -1.2912 | -0.0005 | 0.5232 | -0.5345 | -0.5055 | 2.1198 | 0.3984 | -0.2278 | -0.3633 | 0.2701 | 0.1412 | 0.6379 | -44.4692 | 45.7164 | 66.7634 | 2 | 4.2862 | -0.0454 | 3.431 | 5.5562 | 1.4758 | 3.1657 | -0.5589 | -0.5637 | -0.1714 | 1.2321 | -0.2957 | 0.9925 | -0.0983 | -0.6316 | 0.2053 | 1.5207 | -0.5605 | -0.091 | 0.8315 | 0.0834 | 0.6951 | -52.1884 | 41.3043 | 77.2433 | 3 | 1.1166 | -0.7597 | -2.2676 | 4.1152 | -1.2317 | 6.7786 | -0.6061 | 0.8043 | 0.0571 | 0.019 | 0.5818 | 1.1712 | 0.3628 | -0.9932 | -0.3113 | 0.3978 | -0.0013 | -0.1474 | 0.4826 | 0.0194 | 0.9851 | -53.6617 | 37.6386 | 66.7077 | 4 | 0.158 | -0.2874 | 0.1951 | 0.6849 | -0.3703 | 1.4616 | 0.275 | -0.4041 | -1.009 | -0.057 | -0.0732 | -0.0996 | 1.2581 | -0.3537 | -1.6785 | 0.8435 | -0.5262 | -0.5904 | -0.0962 | -0.0369 | 0.8804 | -44.1632 | 28.3809 | 68.4692 | 5 | 1.8656 | -0.0766 | -0.9623 | 1.5178 | -0.159 | 0.691 | 0.3542 | 0.168 | -0.7017 | -0.1254 | -0.0591 | -0.2956 | 0.5484 | -0.2897 | 0.1115 | 0.4938 | -0.0431 | -0.2914 | 0.301 | 0.0116 | 0.5512 | -35.2531 | 34.1404 | 68.261 | 6 | 2.0387 | -0.0485 | 1.2154 | 2.1848 | -0.6844 | 2.3292 | 0.0866 | 0.2554 | -0.6476 | 0.0832 | 0.1052 | -0.8457 | 0.5483 | 0.5253 | -0.0222 | 0.3443 | 0.0426 | -0.2142 | 0.2981 | 0.0619 | 0.5972 | -17.0036 | 43.1449 | 72.8728 | 7 | 5.7478 | -0.5907 | 0.3814 | 3.1017 | -1.942 | 1.2587 | 0.5598 | 1.0828 | -1.081 | -1.4767 | -0.7509 | -0.0267 | 0.6649 | 0.4436 | 0.0389 | 0.5842 | 0.2332 | -0.1086 | 0.5568 | 0.0949 | 0.3824 | -14.8411 | 46.1702 | 58.5202 | 8 | 0.8178 | -0.0266 | 0.1127 | 0.8698 | 0.1004 | 0.0362 | -0.1961 | 0.4948 | -0.215 | -0.6016 | -0.2092 | -0.5637 | 0.3683 | 0.844 | -0.6255 | 0.788 | 0.2895 | 0.3051 | 0.8706 | 0.1664 | 0.2445 | -10.3137 | 53.5061 | 50.7596 | 9 | 6.9782 | -4.3605 | 3.5981 | 6.4033 | -2.0132 | 1.7926 | -0.1124 | 0.2839 | 0.9526 | 0.6924 | -0.1121 | -1.9251 | -0.2259 | 0.3731 | 0.0351 | 0.5268 | 0.1121 | -0.0297 | 0.7695 | 0.1669 | 0.911 | 0.1174 | 45.8384 | 66.9423 | 10 | 1.2578 | -1.3892 | 1.4733 | 4.1657 | -1.5619 | 2.0636 | 0.3346 | -0.0652 | -1.0709 | 0.0581 | -0.7852 | -0.7129 | 1.6843 | 1.2442 | -3.7525 | 1.3128 | 0.5014 | 0.1316 | 0.5465 | 0.5422 | 1.4773 | -2.0551 | 36.4122 | 67.1559 | 11 | 3.981 | -2.324 | 0.9119 | 2.5541 | -2.6327 | 4.1407 | 0.2612 | 0.3514 | -0.4266 | -0.1774 | 0.1128 | -0.9762 | 0.3453 | 0.0635 | 0.3797 | 0.7385 | 0.0413 | -0.2237 | 0.3498 | 0.0222 | 0.4734 | -13.2439 | 68.3095 | 86.3042 | 12 | 9.3428 | -0.1272 | -1.4364 | 2.1394 | 2.0168 | 3.0648 | 0.4591 | 0.9064 | -0.6197 | -1.081 | -0.3982 | 0.15 | 1.2211 | 0.0643 | -0.0976 | 1.3776 | -0.162 | -0.3429 | 0.6058 | 0.1712 | 0.5679 | -7.4646 | 59.9943 | 95.9995 | 13 | 5.006 | 2.0723 | 0.3499 | 1.7745 | -0.1551 | 0.1313 | -0.2807 | -0.6715 | -0.3979 | 0.3206 | 0.1093 | -0.5515 | 0.2668 | 1.5642 | 0.3517 | 1.0435 | 0.1381 | -0.329 | 0.6648 | 0.021 | 0.5816 | -5.2814 | 70.4882 | 95.5494 | 14 | 3.7178 | 1.8051 | 1.7246 | 3.8943 | 0.9319 | 1.0872 | 0.3627 | -1.2442 | -0.1692 | 1.4172 | -0.4024 | -0.1263 | -0.2915 | -0.5975 | 0.0431 | 0.8549 | -0.2413 | -0.5467 | 0.6943 | -0.0649 | 0.4913 | -16.2536 | 73.0062 | 102.8075 | 15 | 2.2618 | 1.0779 | 1.1264 | 3.8164 | 1.7318 | 1.3284 | -0.0546 | -0.6059 | 0.4655 | 0.5753 | -0.1463 | 0.21 | -0.2264 | -0.4607 | 0.2077 | 0.7144 | 0.0615 | -0.1267 | 0.5003 | -0.0893 | 0.3734 | -24.0639 | 71.9981 | 95.8457 | 16 | 3.5972 | 1.4797 | 1.0998 | 5.3127 | -0.7256 | 1.14 | -0.1335 | -1.0485 | 0.6148 | 0.9276 | -0.3247 | 1.1487 | -0.9542 | -1.0602 | 0.0502 | 0.7144 | 0.1415 | -0.0593 | 0.6659 | -0.1211 | 0.5398 | -41.4072 | 66.4058 | 85.7691 | 17 | 3.4098 | 0.9262 | 0.5135 | 1.1864 | -1.2332 | 2.3238 | -0.0502 | -0.9132 | 1.2542 | 0.6586 | -0.0356 | 0.2531 | -1.5965 | -0.593 | -0.438 | 0.9367 | 0.2036 | -0.1918 | 0.3701 | -0.1462 | 0.7428 | -40.8516 | 78.7791 | 77.6622 | 18 | 0.3174 | 0.4264 | -0.1288 | 0.5871 | -0.0731 | 0.9585 | -0.3715 | -0.1483 | 0.5957 | 0.2856 | 0.1841 | 0.7001 | -0.8149 | -0.5638 | -3.8915 | 1.0859 | 0.3316 | -0.6253 | 0.0266 | 0.1846 | 0.8247 | -42.8449 | 83.9442 | 67.4931 | 19 | 7.3464 | -3.0761 | 0.6225 | 3.5949 | 1.854 | 2.0313 | -1.0973 | -2.0698 | -0.2962 | 0.8468 | 0.2191 | 0.9803 | 0.3246 | -0.6943 | -0.3063 | 0.8035 | 0.652 | -0.2796 | 1.3885 | -0.0802 | 1.1958 | -56.7442 | 72.7417 | 78.1108 | 20 | 1.0503 | 1.3849 | -0.0352 | 2.1643 | -0.8702 | 2.3263 | -0.3002 | -1.4435 | 0.6048 | 1.132 | 0.3811 | 1.0697 | -0.5428 | -0.7323 | 0.5431 | 1.2597 | 0.7116 | 0.1173 | 1.5542 | -0.0487 | 0.8769 | -55.7889 | 75.5592 | 87.2754 |
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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 (RESSEQ -1:27) | 2 | X-RAY DIFFRACTION | 2 | CHAIN A AND (RESSEQ 28:36)3 | X-RAY DIFFRACTION | 3 | CHAIN A AND (RESSEQ 37:60)4 | X-RAY DIFFRACTION | 4 | CHAIN A AND (RESSEQ 61:92)5 | X-RAY DIFFRACTION | 5 | CHAIN A AND (RESSEQ 93:165)6 | X-RAY DIFFRACTION | 6 | CHAIN A AND (RESSEQ 172:279)7 | X-RAY DIFFRACTION | 7 | CHAIN A AND (RESSEQ 280:347)8 | X-RAY DIFFRACTION | 8 | CHAIN A AND (RESSEQ 348:361)9 | X-RAY DIFFRACTION | 9 | CHAIN A AND (RESSEQ 362:386)10 | X-RAY DIFFRACTION | 10 | CHAIN A AND (RESSEQ 387:431)11 | X-RAY DIFFRACTION | 11 | CHAIN B AND (RESSEQ -1:27) | 12 | X-RAY DIFFRACTION | 12 | CHAIN B AND (RESSEQ 28:36)13 | X-RAY DIFFRACTION | 13 | CHAIN B AND (RESSEQ 37:60)14 | X-RAY DIFFRACTION | 14 | CHAIN B AND (RESSEQ 61:92)15 | X-RAY DIFFRACTION | 15 | CHAIN B AND (RESSEQ 93:165)16 | X-RAY DIFFRACTION | 16 | CHAIN B AND (RESSEQ 172:279)17 | X-RAY DIFFRACTION | 17 | CHAIN B AND (RESSEQ 280:347)18 | X-RAY DIFFRACTION | 18 | CHAIN B AND (RESSEQ 348:361)19 | X-RAY DIFFRACTION | 19 | CHAIN B AND (RESSEQ 362:386)20 | X-RAY DIFFRACTION | 20 | CHAIN B AND ( | | | | | | | | | | | | | | | | | |
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