Software | Name | Version | Classification |
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PHENIX | 1.9_1692refinementHKL-2000 | | data reductionHKL-2000 | | data scalingPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ycb Resolution: 1.502→41.338 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.23 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1574 | 3140 | 4.77 % | Same as 4YCB |
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Rwork | 0.1389 | - | - | - |
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obs | 0.1398 | 65888 | 99.92 % | - |
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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: 1.502→41.338 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2305 | 0 | 55 | 317 | 2677 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.008 | 2658 | X-RAY DIFFRACTION | f_angle_d1.087 | 3672 | X-RAY DIFFRACTION | f_dihedral_angle_d12.298 | 1011 | X-RAY DIFFRACTION | f_chiral_restr0.043 | 434 | X-RAY DIFFRACTION | f_plane_restr0.006 | 476 | | | | | |
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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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1.5023-1.5257 | 0.2087 | 139 | 0.1956 | 2768 | X-RAY DIFFRACTION | 98 | 1.5257-1.5508 | 0.1865 | 141 | 0.1755 | 2823 | X-RAY DIFFRACTION | 100 | 1.5508-1.5775 | 0.1945 | 141 | 0.1634 | 2828 | X-RAY DIFFRACTION | 100 | 1.5775-1.6062 | 0.1989 | 140 | 0.1619 | 2801 | X-RAY DIFFRACTION | 100 | 1.6062-1.6371 | 0.1824 | 142 | 0.1542 | 2816 | X-RAY DIFFRACTION | 100 | 1.6371-1.6705 | 0.1593 | 141 | 0.1416 | 2827 | X-RAY DIFFRACTION | 100 | 1.6705-1.7068 | 0.1569 | 141 | 0.14 | 2824 | X-RAY DIFFRACTION | 100 | 1.7068-1.7465 | 0.1653 | 141 | 0.145 | 2822 | X-RAY DIFFRACTION | 100 | 1.7465-1.7902 | 0.1468 | 139 | 0.1355 | 2824 | X-RAY DIFFRACTION | 100 | 1.7902-1.8386 | 0.1596 | 145 | 0.1381 | 2838 | X-RAY DIFFRACTION | 100 | 1.8386-1.8927 | 0.154 | 137 | 0.1331 | 2831 | X-RAY DIFFRACTION | 100 | 1.8927-1.9538 | 0.1381 | 146 | 0.1263 | 2823 | X-RAY DIFFRACTION | 100 | 1.9538-2.0236 | 0.1346 | 140 | 0.1307 | 2837 | X-RAY DIFFRACTION | 100 | 2.0236-2.1046 | 0.1474 | 142 | 0.1303 | 2840 | X-RAY DIFFRACTION | 100 | 2.1046-2.2004 | 0.1516 | 144 | 0.1277 | 2864 | X-RAY DIFFRACTION | 100 | 2.2004-2.3164 | 0.1512 | 144 | 0.1335 | 2853 | X-RAY DIFFRACTION | 100 | 2.3164-2.4615 | 0.156 | 145 | 0.1349 | 2854 | X-RAY DIFFRACTION | 100 | 2.4615-2.6516 | 0.1752 | 139 | 0.1445 | 2874 | X-RAY DIFFRACTION | 100 | 2.6516-2.9183 | 0.1798 | 148 | 0.1443 | 2880 | X-RAY DIFFRACTION | 100 | 2.9183-3.3405 | 0.1472 | 142 | 0.1382 | 2903 | X-RAY DIFFRACTION | 100 | 3.3405-4.208 | 0.1464 | 148 | 0.1285 | 2939 | X-RAY DIFFRACTION | 100 | 4.208-41.3539 | 0.1505 | 155 | 0.1405 | 3079 | X-RAY DIFFRACTION | 100 |
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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 | 1.9888 | -1.7401 | -0.2546 | 2.0396 | -1.5576 | 6.1627 | 0.0323 | -0.2345 | 0.3686 | 0.0151 | 0.0218 | 0.1302 | -0.1393 | -0.068 | 0.0142 | 0.0613 | 0.0169 | -0.0108 | 0.0961 | -0.0443 | 0.1331 | -6.254 | 29.6668 | 35.8511 | 2 | 7.7125 | 5.6366 | 0.0516 | 4.412 | -0.1283 | 1.6528 | 0.116 | -0.5107 | -0.0235 | 0.2416 | -0.2157 | -0.0648 | 0.088 | -0.0192 | 0.0557 | 0.1339 | 0.0044 | -0.0099 | 0.1453 | -0.0218 | 0.1002 | -1.1536 | 22.7178 | 41.1222 | 3 | 6.3867 | 4.1757 | 1.848 | 3.5248 | 1.3515 | 0.8958 | 0.1116 | -0.2476 | 0.1814 | 0.1848 | -0.1463 | 0.0027 | 0.0071 | -0.0673 | 0.0441 | 0.1045 | -0.0021 | -0.0027 | 0.1111 | -0.0376 | 0.095 | -8.9754 | 26.9136 | 36.1295 | 4 | 6.3243 | 5.8031 | -3.0521 | 6.6394 | -2.8142 | 1.6886 | -0.0598 | 0.0764 | 0.5123 | -0.0643 | 0.0907 | 0.3531 | -0.07 | -0.1453 | -0.0399 | 0.1063 | 0.0287 | -0.0229 | 0.1013 | -0.0263 | 0.1654 | -16.6389 | 30.4042 | 28.4005 | 5 | 1.4583 | -0.3113 | 0.2133 | 1.6211 | 0.5503 | 1.4203 | -0.0333 | 0.0047 | 0.2141 | -0.0943 | -0.0441 | 0.0628 | -0.0954 | -0.0479 | 0.0441 | 0.0733 | -0.0001 | -0.0155 | 0.0665 | -0.0072 | 0.1063 | -7.9669 | 26.8684 | 26.9336 | 6 | 2.8543 | -2.5694 | -1.6851 | 2.4288 | 1.0721 | 2.7098 | 0.202 | -0.5881 | -0.4458 | 0.7736 | -0.1834 | -0.2516 | 0.2142 | -0.0894 | 0.1372 | 0.1976 | -0.0531 | -0.0371 | 0.1557 | 0.0446 | 0.1263 | -4.4764 | 5.8565 | 34.6278 | 7 | 1.6057 | 1.2284 | 0.3134 | 2.3613 | 0.3404 | 1.0405 | -0.0238 | -0.0004 | 0.074 | 0.0268 | -0.0133 | 0.0154 | -0.0603 | 0.014 | 0.0418 | 0.0591 | 0.0111 | -0.0029 | 0.0725 | -0.0032 | 0.0693 | 1.1214 | 21.9784 | 26.6292 | 8 | 3.3469 | -4.7397 | 1.1154 | 8.5556 | -1.3142 | 1.1648 | 0.0915 | 0.0592 | 0.1046 | -0.1963 | -0.0454 | -0.0384 | -0.0423 | 0.1105 | -0.035 | 0.1101 | -0.0245 | -0.0352 | 0.1077 | -0.0229 | 0.1213 | 14.8711 | 32.3662 | 34.8523 | 9 | 7.4389 | -4.4782 | 5.3402 | 5.5932 | -6.0736 | 8.1167 | 0.0552 | -0.2213 | -0.2282 | 0.4723 | -0.0564 | -0.1238 | 0.2573 | -0.1569 | -0.1504 | 0.2028 | 0.003 | -0.0531 | 0.1493 | -0.0306 | 0.1257 | 24.0743 | 15.6416 | 42.6252 | 10 | 3.1621 | 0.3162 | 0.5668 | 0.1512 | 0.6719 | 3.2646 | 0.0831 | 0.2381 | 0.224 | -0.3431 | -0.0056 | -0.1499 | -0.1006 | 0.0745 | -0.05 | 0.15 | -0.0254 | 0.0127 | 0.1122 | 0.0358 | 0.103 | 13.5958 | 27.546 | 11.4363 | 11 | 3.8955 | -3.5006 | -1.1498 | 8.6324 | 2.2896 | 2.3041 | 0.051 | 0.3467 | 0.0225 | -0.3472 | -0.1373 | 0.1748 | -0.0429 | -0.159 | 0.0894 | 0.1663 | -0.0182 | -0.0251 | 0.1461 | 0.0241 | 0.0675 | 6.8416 | 22.2204 | 6.0692 | 12 | 1.4009 | -0.4838 | -0 | 1.582 | -0.2286 | 0.8604 | -0.0039 | 0.0657 | 0.1799 | -0.0567 | -0.0529 | -0.1429 | -0.0989 | 0.122 | 0.0586 | 0.1044 | -0.0191 | -0.0108 | 0.083 | 0.017 | 0.0936 | 16.7311 | 24.5217 | 17.9484 | 13 | 6.6464 | 3.3982 | 1.2369 | 5.4934 | 0.2451 | 2.5921 | -0.0169 | 0.5718 | -0.2721 | -0.9381 | 0.0373 | 0.3186 | 0.1908 | 0.1951 | 0.0741 | 0.1997 | 0.0241 | -0.022 | 0.1404 | -0.026 | 0.1216 | 5.8458 | 4.6642 | 12.2801 | 14 | 1.0705 | -0.5121 | 0.0619 | 2.4826 | 0.0305 | 1.1709 | -0.0299 | 0.0182 | 0.0631 | -0.0579 | 0.0213 | 0.0012 | -0.0666 | -0.0019 | 0.0117 | 0.0521 | -0.0106 | -0.0052 | 0.0683 | -0.0009 | 0.0574 | 4.5534 | 21.7022 | 20.6647 | 15 | 5.0818 | 3.0892 | 1.216 | 2.5487 | 0.0172 | 1.4391 | -0.1942 | 0.0842 | 0.4802 | -0.0216 | 0.1746 | 0.4874 | -0.3029 | -0.1664 | 0.0902 | 0.2339 | 0.0275 | -0.0638 | 0.1649 | 0.0619 | 0.2577 | -6.9809 | 34.9815 | 12.15 | 16 | 2.8603 | 3.4544 | 0.9419 | 7.4928 | 3.3078 | 3.109 | -0.1064 | -0.0183 | -0.061 | -0.1447 | 0.0886 | 0.4261 | -0.1144 | -0.1203 | 0.0528 | 0.1786 | -0.025 | -0.0431 | 0.2027 | 0.0635 | 0.1428 | -20.8045 | 19.9928 | 4.0903 |
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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 20 through 30 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 31 through 46 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 47 through 61 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 62 through 72 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 73 through 107 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 108 through 114 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 115 through 154 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 155 through 171 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 172 through 180 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 20 through 30 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 31 through 46 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 47 through 107 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 108 through 114 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 115 through 154 )15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid 155 through 171 )16 | X-RAY DIFFRACTION | 16 | chain 'B' | | | | | | | | | | | | | | | |
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