Software | Name | Version | Classification |
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Blu-Ice | | data collectionPHASER | | phasingPHENIX | (phenix.refine: 1.7_650)refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→38.95 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 18.92 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.186 | 2143 | 5.08 % |
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Rwork | 0.1626 | - | - |
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obs | 0.1638 | 42144 | 93.92 % |
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all | - | 42144 | - |
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Solvent computation | Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.685 Å2 / ksol: 0.414 e/Å3 |
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Refinement step | Cycle: LAST / Resolution: 1.96→38.95 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2883 | 0 | 93 | 190 | 3166 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 3083 | X-RAY DIFFRACTION | f_angle_d1.29 | 4204 | X-RAY DIFFRACTION | f_dihedral_angle_d15.425 | 1093 | X-RAY DIFFRACTION | f_chiral_restr0.064 | 427 | X-RAY DIFFRACTION | f_plane_restr0.004 | 538 | | | | | |
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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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1.96-2.0056 | 0.2579 | 122 | 0.2173 | 2414 | X-RAY DIFFRACTION | 86 | 2.0056-2.0558 | 0.2396 | 131 | 0.1972 | 2502 | X-RAY DIFFRACTION | 88 | 2.0558-2.1113 | 0.213 | 126 | 0.1905 | 2494 | X-RAY DIFFRACTION | 90 | 2.1113-2.1735 | 0.2068 | 140 | 0.1891 | 2538 | X-RAY DIFFRACTION | 90 | 2.1735-2.2436 | 0.1955 | 137 | 0.1761 | 2573 | X-RAY DIFFRACTION | 91 | 2.2436-2.3238 | 0.2079 | 138 | 0.176 | 2597 | X-RAY DIFFRACTION | 92 | 2.3238-2.4168 | 0.199 | 137 | 0.1759 | 2624 | X-RAY DIFFRACTION | 93 | 2.4168-2.5268 | 0.2061 | 145 | 0.1809 | 2636 | X-RAY DIFFRACTION | 94 | 2.5268-2.66 | 0.2 | 141 | 0.1771 | 2674 | X-RAY DIFFRACTION | 95 | 2.66-2.8266 | 0.1971 | 152 | 0.1834 | 2738 | X-RAY DIFFRACTION | 97 | 2.8266-3.0448 | 0.2273 | 152 | 0.1745 | 2767 | X-RAY DIFFRACTION | 98 | 3.0448-3.351 | 0.1938 | 155 | 0.1619 | 2790 | X-RAY DIFFRACTION | 98 | 3.351-3.8356 | 0.184 | 165 | 0.1435 | 2810 | X-RAY DIFFRACTION | 99 | 3.8356-4.831 | 0.1457 | 137 | 0.1242 | 2877 | X-RAY DIFFRACTION | 99 | 4.831-38.9574 | 0.1655 | 165 | 0.1727 | 2967 | 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 | 2.3362 | 0.2448 | 0.816 | 1.6353 | -0.4277 | 0.7393 | -0.0881 | -0.4795 | -0.2468 | 0.3516 | 0.0908 | -0.1957 | 0.079 | 0.571 | 0.0051 | 0.3366 | 0.0609 | -0.0398 | 0.5212 | 0.0149 | 0.2783 | 49.1668 | 46.7786 | 74.0223 | 2 | 0.0951 | -0.0583 | -0.0788 | 0.3303 | -0.2502 | 0.3981 | -0.2116 | -0.4211 | -0.0328 | 0.3977 | 0.1689 | -0.2616 | 0.014 | 0.201 | 0.1924 | 0.5816 | 0.4289 | 0.0497 | 0.9051 | 0.5341 | 0.092 | 50.4089 | 40.1926 | 83.2251 | 3 | 0.5697 | 0.2906 | 0.4755 | 0.5501 | 0.2353 | 0.5148 | -0.4062 | -0.2149 | -1.0154 | 0.0378 | -0.0877 | 0.1326 | 0.4269 | 0.3176 | -0.0846 | 0.3695 | 0.1413 | 0.1081 | 0.4662 | 0.1858 | 0.4443 | 49.4791 | 35.9687 | 70.6871 | 4 | 1.2779 | -0.9372 | -0.4731 | 1.7949 | -0.5905 | 3.6252 | -0.4903 | -1.0447 | -0.5331 | 0.4668 | 0.3304 | 0.7527 | -0.4841 | -0.1677 | -0.1316 | 0.4783 | 0.1582 | 0.1431 | 0.6711 | 0.2021 | 0.4697 | 39.9671 | 42.5993 | 79.7925 | 5 | 1.8989 | -0.093 | -0.2816 | 1.0488 | -0.1415 | 0.169 | -0.2471 | -0.707 | -0.059 | 0.4975 | 0.0876 | 0.0689 | -0.1542 | 0.5347 | 0.0542 | 0.3578 | 0.0205 | 0.041 | 0.4563 | 0.0024 | 0.2392 | 44.5586 | 53.4996 | 73.6884 | 6 | 1.1988 | 0.2786 | -0.6935 | 1.5677 | 0.1448 | 1.7973 | -0.1232 | -0.6385 | 0.0994 | -0.0465 | -0.007 | -0.361 | -0.1326 | 0.1746 | 0.0283 | 0.2871 | 0.0159 | 0.0231 | 0.3814 | 0.0284 | 0.3043 | 49.2314 | 59.1762 | 59.8506 | 7 | 0.2351 | 0.0344 | -0.0155 | 1.0816 | -0.497 | 0.3357 | 0.0529 | 0.0138 | 0.0824 | -0.3133 | -0.2141 | -0.1307 | 0.1116 | -0.1634 | 0.088 | 0.3231 | 0.0371 | 0.0202 | 0.349 | 0.011 | 0.2408 | 40.5997 | 56.9622 | 57.0137 | 8 | 1.1856 | -1.3068 | -0.0901 | 2.4038 | 0.6937 | 1.2234 | 0.3677 | 0.4668 | -0.2556 | -0.6025 | -0.5221 | 0.0597 | -0.1064 | -0.1648 | 0.0552 | 0.3522 | 0.039 | -0.0244 | 0.3893 | -0.0435 | 0.3016 | 34.6391 | 53.8076 | 59.603 | 9 | 0.9587 | -0.0606 | -0.4003 | 0.1822 | 0.4754 | 1.4059 | -0.042 | 0.0596 | -0.144 | -0.1508 | -0.2001 | 0.0303 | -0.199 | -0.2433 | 0.0792 | 0.3393 | 0.009 | 0.0027 | 0.4039 | -0.0334 | 0.2946 | 30.5159 | 56.2757 | 65.2568 | 10 | 1.1786 | 0.6851 | 0.0609 | 2.0975 | -0.3524 | 0.1297 | 0.041 | -0.3127 | 0.0066 | 0.5243 | 0.0176 | -0.0244 | -0.1399 | 0.0058 | -0.0355 | 0.3409 | -0.0151 | 0.0322 | 0.361 | -0.055 | 0.2797 | 39.7539 | 59.4395 | 70.9701 | 11 | 0.2246 | -0.3387 | -0.0849 | 0.391 | 0.2545 | 0.7274 | -0.0766 | 0.0077 | -0.0238 | -0.0102 | 0.0192 | -0.1162 | -0.1894 | -0.0799 | 0.005 | 0.3697 | -0.0151 | 0.013 | 0.3727 | -0.1034 | 0.3257 | 34.6496 | 65.5572 | 71.279 | 12 | 0.0145 | -0.0506 | -0.0651 | 2.5772 | -1.0924 | 0.9439 | -0.0434 | 0.3441 | -0.4631 | -0.2305 | 0.3504 | 1.2473 | 0.6513 | -0.564 | -0.0507 | 0.3408 | -0.0858 | 0.0309 | 0.4011 | -0.0999 | 0.5439 | 22.7259 | 50.3626 | 69.5348 | 13 | 1.2774 | -0.1384 | -0.405 | 2.5652 | -0.8688 | 1.0781 | 0.2655 | 0.1024 | -0.069 | 0.2896 | -0.4309 | -0.3009 | -0.2757 | -0.0666 | 0.0471 | 0.3846 | 0.0401 | 0.0188 | 0.342 | -0.0159 | 0.2813 | 31.6611 | 65.9992 | 68.2724 | 14 | 0.6625 | -0.44 | -0.0428 | 0.6864 | -0.5492 | 1.9501 | 0.158 | 0.1455 | 0.0511 | -0.1573 | -0.284 | 0.2297 | -0.8045 | -0.2019 | 0.0877 | 0.462 | 0.1032 | -0.0608 | 0.3217 | -0.0186 | 0.2982 | 15.1664 | 81.0656 | 74.8136 | 15 | 1.1465 | 0.342 | -0.5096 | 0.8487 | -0.8057 | 0.8923 | 0.1076 | -0.0367 | -0.3121 | -0.2313 | -0.5288 | 0.7697 | -0.3959 | -0.5736 | -0.2739 | 0.4294 | 0.1719 | -0.1211 | 0.3843 | -0.1646 | 0.4365 | 6.8996 | 81.0312 | 81.6211 | 16 | 1.9961 | -0.8482 | 0.5431 | 1.7142 | 1.4324 | 2.0743 | 0.0969 | 0.5559 | -0.4768 | -0.3407 | -0.4057 | 0.322 | -0.352 | -0.0052 | 0.0627 | 0.3996 | 0.0874 | -0.08 | 0.3996 | -0.1041 | 0.3632 | 13.8099 | 71.4349 | 72.8522 | 17 | 1.0066 | 0.074 | 0.7442 | 0.6712 | 0.5243 | 0.6539 | -0.1445 | 0.2227 | 0.0352 | -0.2969 | 0.1064 | 0.0136 | -0.4525 | 0.2479 | 0.016 | 0.3857 | -0.0021 | -0.0236 | 0.2884 | -0.0287 | 0.2373 | 25.593 | 78.4009 | 83.2803 | 18 | 3.2805 | -1.4389 | -1.5033 | 1.3293 | -0.5044 | 2.602 | 0.4544 | 0.6363 | 0.2263 | -0.4955 | -0.0503 | -0.1572 | 0.4681 | 0.6074 | -0.1625 | 0.3681 | 0.0653 | -0.0366 | 0.4489 | -0.0545 | 0.2905 | 35.5219 | 72.1351 | 93.4826 | 19 | 2.2084 | 0.6326 | -1.212 | 2.9264 | -0.8088 | 0.7907 | -0.2634 | -0.8136 | 0.2641 | 0.3952 | -0.1288 | -0.3772 | -0.3559 | -0.3423 | 0.0097 | 0.3656 | 0.0358 | -0.0288 | 0.3903 | -0.0938 | 0.2204 | 23.1016 | 74.3588 | 97.5309 | 20 | 2.3793 | -1.5725 | -0.4269 | 1.8738 | -0.3125 | 1.4399 | -0.3526 | -0.6459 | -0.1408 | 0.4691 | 0.3929 | 0.1938 | 0.0931 | 0.1711 | -0.022 | 0.3764 | 0.0381 | 0.0031 | 0.3397 | -0.0137 | 0.3023 | 24.8425 | 66.7828 | 93.3753 | 21 | 0.5076 | -0.2944 | 0.1223 | 0.8511 | -0.0711 | 1.3881 | -0.0823 | 0.1016 | -0.1298 | 0.1513 | -0.109 | 0.0433 | 0.2988 | 0.2699 | 0.0386 | 0.3284 | -0.0058 | 0.006 | 0.3252 | -0.0076 | 0.251 | 27.6184 | 62.6443 | 87.7608 | 22 | 0.4202 | 0.3349 | -0.1386 | 0.8163 | -0.0875 | 0.8162 | -0.1247 | -0.0497 | 0.107 | -0.3081 | -0.0115 | -0.0024 | 0.0216 | 0.3544 | 0.0381 | 0.3326 | -0.0032 | 0.0431 | 0.3775 | -0.0467 | 0.2612 | 33.6179 | 69.7117 | 81.9271 | 23 | 1.2837 | -0.4217 | 0.1954 | 0.5785 | 0.1391 | 2.0445 | -0.0929 | 0.2158 | -0.278 | 0.0089 | 0.1774 | 0.0997 | 0.6234 | 0.1789 | -0.0009 | 0.4218 | -0.0206 | 0.0341 | 0.3788 | -0.0424 | 0.3283 | 29.4369 | 58.6402 | 84.0104 |
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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 1:17)2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 18:28)3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 29:44)4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resseq 45:62)5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resseq 63:80)6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resseq 81:93)7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resseq 94:111)8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resseq 112:126)9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resseq 127:141)10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resseq 142:155)11 | X-RAY DIFFRACTION | 11 | chain 'A' and (resseq 156:166)12 | X-RAY DIFFRACTION | 12 | chain 'A' and (resseq 167:174)13 | X-RAY DIFFRACTION | 13 | chain 'A' and (resseq 175:183)14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resseq 1:28)15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resseq 29:44)16 | X-RAY DIFFRACTION | 16 | chain 'B' and (resseq 45:62)17 | X-RAY DIFFRACTION | 17 | chain 'B' and (resseq 63:90)18 | X-RAY DIFFRACTION | 18 | chain 'B' and ( | | | | | | | | | | | | | | | | | |
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