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: FOURIER SYNTHESIS Starting model: 4ycb chain A Resolution: 1.808→42.574 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.34 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1677 | 1810 | 4.77 % | Same as 4z7j |
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Rwork | 0.1365 | - | - | - |
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obs | 0.1379 | 37934 | 99.58 % | - |
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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: 1.808→42.574 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2314 | 0 | 26 | 388 | 2728 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 2501 | X-RAY DIFFRACTION | f_angle_d1.021 | 3440 | X-RAY DIFFRACTION | f_dihedral_angle_d11.957 | 926 | X-RAY DIFFRACTION | f_chiral_restr0.044 | 417 | X-RAY DIFFRACTION | f_plane_restr0.004 | 445 | | | | | |
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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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1.8076-1.8564 | 0.2047 | 130 | 0.1641 | 2573 | X-RAY DIFFRACTION | 95 | 1.8564-1.911 | 0.1841 | 139 | 0.144 | 2761 | X-RAY DIFFRACTION | 100 | 1.911-1.9727 | 0.1588 | 138 | 0.1314 | 2753 | X-RAY DIFFRACTION | 100 | 1.9727-2.0432 | 0.1655 | 137 | 0.1303 | 2759 | X-RAY DIFFRACTION | 100 | 2.0432-2.125 | 0.1665 | 136 | 0.1342 | 2748 | X-RAY DIFFRACTION | 100 | 2.125-2.2218 | 0.1818 | 139 | 0.1307 | 2757 | X-RAY DIFFRACTION | 100 | 2.2218-2.3389 | 0.1707 | 139 | 0.1317 | 2768 | X-RAY DIFFRACTION | 100 | 2.3389-2.4854 | 0.1494 | 138 | 0.1331 | 2774 | X-RAY DIFFRACTION | 100 | 2.4854-2.6773 | 0.1818 | 140 | 0.1438 | 2788 | X-RAY DIFFRACTION | 100 | 2.6773-2.9466 | 0.1863 | 140 | 0.1474 | 2796 | X-RAY DIFFRACTION | 100 | 2.9466-3.3729 | 0.1551 | 142 | 0.1367 | 2821 | X-RAY DIFFRACTION | 100 | 3.3729-4.2489 | 0.1547 | 141 | 0.1264 | 2839 | X-RAY DIFFRACTION | 100 | 4.2489-42.5856 | 0.1676 | 151 | 0.139 | 2987 | 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 | 2.7322 | -1.5956 | -0.8394 | 1.9071 | -1.737 | 5.3563 | 0.0516 | -0.3193 | 0.3156 | 0.2168 | -0.0769 | -0.0593 | -0.2214 | 0.0349 | 0.0669 | 0.0798 | 0.0202 | -0.0194 | 0.1063 | -0.0463 | 0.1288 | -5.8213 | 30.0651 | 35.7293 | 2 | 8.534 | 5.8775 | 0.6067 | 4.4944 | 0.2346 | 2.9471 | 0.081 | -0.5513 | 0.0083 | 0.1894 | -0.2153 | 0.0473 | 0.1846 | -0.0595 | 0.0986 | 0.1467 | 0.0155 | 0.0027 | 0.1676 | -0.0231 | 0.1105 | -0.7812 | 22.8327 | 40.9882 | 3 | 8.8316 | 5.0128 | 1.548 | 3.9749 | 0.8254 | 0.5235 | 0.1084 | -0.163 | 0.2 | 0.2223 | -0.1001 | -0.019 | 0.0199 | -0.0155 | -0.0181 | 0.1274 | 0.0062 | -0.0032 | 0.113 | -0.0346 | 0.0854 | -8.1173 | 27.4836 | 36.1 | 4 | 5.1897 | 5.5454 | -1.7586 | 7.7549 | -2.4711 | 0.7931 | -0.0341 | 0.2145 | 0.4956 | -0.1318 | 0.1164 | 0.4228 | -0.092 | -0.054 | -0.0824 | 0.1076 | 0.0395 | -0.0193 | 0.1063 | -0.0221 | 0.1494 | -16.4767 | 30.5052 | 28.3314 | 5 | 1.9173 | -0.2986 | 0.307 | 5.4138 | 0.4693 | 1.5785 | -0.0015 | 0.0247 | 0.1812 | -0.0421 | -0.091 | 0.0116 | -0.0864 | -0.0874 | 0.0834 | 0.0687 | -0.0012 | 0.0047 | 0.0916 | -0.0162 | 0.0886 | -7.5734 | 26.8278 | 27.0653 | 6 | 5.6605 | 0.8197 | -3.474 | 2.422 | 0.146 | 2.3184 | 0.1215 | -0.6128 | -0.8529 | 0.7431 | -0.1859 | -0.4958 | 0.2915 | 0.1002 | 0.2495 | 0.2289 | -0.0485 | -0.0503 | 0.2059 | 0.0596 | 0.2132 | -4.4901 | 5.8218 | 34.3792 | 7 | 1.5442 | 0.9447 | 0.0317 | 2.3883 | -0.2131 | 1.025 | -0.0161 | 0.013 | 0.0422 | 0.0004 | -0.034 | 0.0156 | -0.0412 | -0.0072 | 0.0552 | 0.0683 | 0.017 | -0.0051 | 0.0904 | -0.0123 | 0.075 | 0.5077 | 21.1586 | 25.9034 | 8 | 5.3661 | -4.8521 | 3.0387 | 5.1314 | -2.6878 | 1.91 | 0.1202 | 0.201 | -0.0365 | -0.1331 | -0.1161 | 0.0445 | 0.0269 | 0.1525 | 0.0424 | 0.1182 | -0.0243 | -0.0209 | 0.1057 | -0.0306 | 0.1233 | 15.0543 | 32.1296 | 35.1073 | 9 | 3.5836 | -2.4403 | -2.4324 | 3.309 | -0.1066 | 3.6193 | 0.1375 | -0.4037 | -0.1686 | 0.8151 | -0.2124 | -0.4103 | 0.5536 | 0.2051 | 0.1672 | 0.3217 | -0.0079 | -0.1008 | 0.2091 | -0.0229 | 0.2006 | 24.3178 | 14.4818 | 43.2515 | 10 | 3.3208 | 0.6711 | 0.4125 | 0.205 | 0.5909 | 3.7418 | 0.1154 | 0.2791 | 0.2301 | -0.4103 | -0.015 | -0.2485 | -0.1293 | 0.0883 | -0.0256 | 0.1447 | -0.0202 | 0.0062 | 0.1223 | 0.0432 | 0.1015 | 13.501 | 27.456 | 11.2887 | 11 | 4.257 | -3.183 | -1.2557 | 7.1512 | 2.5397 | 2.3206 | 0.0306 | 0.4018 | 0.072 | -0.3786 | -0.1677 | 0.1285 | -0.1047 | -0.1957 | 0.1371 | 0.2053 | -0.0244 | -0.0272 | 0.1914 | 0.0304 | 0.0915 | 6.7165 | 22.3289 | 6.0011 | 12 | 1.5787 | -0.5035 | -0.0147 | 2.1033 | -0.3856 | 1.0064 | 0.0151 | 0.0815 | 0.1336 | -0.11 | -0.0478 | -0.1322 | -0.0543 | 0.1214 | 0.0446 | 0.1295 | -0.0194 | -0.0066 | 0.1027 | 0.0175 | 0.101 | 16.4902 | 24.653 | 17.5517 | 13 | 5.2484 | 4.0856 | -0.2479 | 3.1902 | -0.1532 | 5.0034 | -0.1008 | 0.6348 | -0.3695 | -0.8312 | 0.151 | 0.5168 | 0.435 | 0.0886 | 0.1372 | 0.23 | 0.0321 | -0.0314 | 0.1902 | -0.0411 | 0.1594 | 5.8173 | 4.7036 | 12.009 | 14 | 0.7133 | -0.1224 | 0.0837 | 3.0679 | 0.6795 | 0.8454 | -0.0181 | 0.0532 | 0.0352 | -0.1371 | -0.0025 | 0.0863 | -0.0549 | -0.0015 | 0.0263 | 0.0702 | -0.0067 | -0.0009 | 0.102 | 0.0077 | 0.0793 | 4.4416 | 20.9327 | 20.2941 | 15 | 6.3412 | 5.7312 | 3.6084 | 5.4157 | 3.2637 | 2.7147 | -0.2449 | -0.1631 | 0.575 | -0.2901 | 0.0109 | 0.6995 | -0.2146 | -0.3485 | 0.2441 | 0.2895 | 0.022 | -0.0942 | 0.2233 | 0.0675 | 0.3394 | -6.5898 | 35.5668 | 12.256 | 16 | 6.2188 | 0.8858 | -3.5635 | 7.0429 | -0.0222 | 2.5948 | -0.2734 | -0.0756 | -0.1232 | -0.6328 | -0.1223 | 0.7363 | -0.2142 | -0.188 | 0.3974 | 0.2704 | -0.0422 | -0.0868 | 0.2571 | 0.0697 | 0.1808 | -20.771 | 20.2263 | 4.0508 |
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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 179 )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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