Software | Name | Version | Classification | NB |
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DENZO | | data reduction | SCALEPACK | | data scaling | PHENIX | 1.8.4_1496refinement | PDB_EXTRACT | 3.14 | data extraction | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.444→43.275 Å / FOM work R set: 0.785 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 27.17 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2632 | 1076 | 10.01 % |
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Rwork | 0.2028 | - | - |
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obs | 0.2088 | 10754 | 93.11 % |
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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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Displacement parameters | Biso max: 122.31 Å2 / Biso mean: 52.42 Å2 / Biso min: 24.34 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.444→43.275 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2213 | 0 | 60 | 46 | 2319 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.008 | 2296 | X-RAY DIFFRACTION | f_angle_d1.101 | 3052 | X-RAY DIFFRACTION | f_chiral_restr0.048 | 325 | X-RAY DIFFRACTION | f_plane_restr0.006 | 386 | X-RAY DIFFRACTION | f_dihedral_angle_d15.586 | 911 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.4444-2.5556 | 0.2957 | 106 | 0.2497 | 957 | 1063 | 76 | 2.5556-2.6903 | 0.3004 | 127 | 0.257 | 1137 | 1264 | 89 | 2.6903-2.8589 | 0.3175 | 139 | 0.2666 | 1250 | 1389 | 98 | 2.8589-3.0795 | 0.3119 | 140 | 0.2403 | 1259 | 1399 | 99 | 3.0795-3.3893 | 0.2978 | 140 | 0.2205 | 1270 | 1410 | 98 | 3.3893-3.8795 | 0.2572 | 140 | 0.1967 | 1253 | 1393 | 97 | 3.8795-4.8867 | 0.203 | 140 | 0.1612 | 1259 | 1399 | 96 | 4.8867-43.2815 | 0.2588 | 144 | 0.1882 | 1293 | 1437 | 93 |
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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 | 3.0261 | 1.5874 | 1.0587 | 1.7063 | -1.8312 | 6.7915 | 0.2547 | -0.2925 | 0.0402 | 0.5018 | 0.3974 | 1.294 | 0.5668 | -0.3536 | -0.5515 | 0.4548 | -0.036 | -0.0003 | 0.3569 | 0.0595 | 0.5829 | -12.1218 | 35.2389 | 20.0116 | 2 | 7.8201 | 1.9397 | 1.7108 | 9 | 0.2236 | 7.3839 | -0.4391 | -0.7028 | -0.3198 | 0.2196 | 1.0564 | -0.7308 | 0.2517 | 0.6181 | -0.7244 | 0.3758 | 0.0574 | -0.0455 | 0.3489 | -0.0792 | 0.4611 | -8.2671 | 27.1219 | 10.8039 | 3 | 1.3881 | 0.5191 | -1.172 | 1.593 | -0.6251 | 1.5888 | -0.0494 | -0.099 | 0.0214 | -0.1048 | 0.035 | 0.0356 | 0.0519 | -0.0334 | -0.0289 | 0.3328 | 0.0687 | 0.0209 | 0.3246 | -0.0279 | 0.3454 | -13.5901 | 23.6685 | -9.9006 | 4 | 2.1375 | -0.0544 | 0.1902 | 2.2532 | 0.8691 | 1.9374 | -0.0942 | -0.1474 | -0.1102 | -0.2841 | -0.2135 | -0.2935 | -0.1228 | 0.3935 | 0.3574 | 0.3225 | 0.0218 | 0.0928 | 0.5427 | -0.0393 | 0.4361 | 0.2848 | 32.5599 | -16.7136 | 5 | 2.8655 | -0.0429 | -0.8417 | 3.6341 | -1.4299 | 3.9155 | 0.0121 | 0.0429 | -0.2775 | -0.7917 | -0.3284 | -0.886 | 0.7596 | 1.0429 | -0.1156 | 0.4018 | 0.0455 | 0.0183 | 0.443 | 0.0194 | 0.498 | 0.0726 | 15.3267 | -11.0374 | 6 | 4.1956 | -1.0759 | -0.9716 | 1.3628 | 0.1118 | 1.55 | 0.3067 | 0.5633 | -0.0463 | -0.0208 | -0.0323 | -0.2662 | -0.0283 | 0.3262 | -0.2104 | 0.493 | 0.0043 | 0.0307 | 0.4529 | -0.2087 | 0.4344 | -7.7605 | 14.4227 | -19.352 | 7 | 3.1548 | 0.8491 | -1.0805 | 3.8509 | -1.2698 | 3.124 | -0.3228 | 0.5772 | -0.5127 | -0.2474 | 0.4237 | 0.1289 | 0.8663 | 0.2581 | -0.5667 | 0.5058 | 0.0043 | 0.063 | 0.5205 | -0.096 | 0.3329 | -8.3598 | 24.5877 | -22.4046 | 8 | 1.5209 | -0.9708 | -1.3491 | 1.0082 | 0.0839 | 2.5263 | 0.1957 | 0.8475 | -0.4578 | 0.54 | 0.3794 | 0.4602 | -0.2004 | 2.3044 | -0.2378 | 0.8973 | -0.0569 | 0.148 | 1.508 | -0.2138 | 0.8219 | 6.9168 | 25.8073 | -25.7523 | 9 | 4.1454 | 1.3885 | -0.1395 | 0.7336 | -0.603 | 1.317 | 0.144 | 0.2217 | 0.385 | 0.1472 | -0.0594 | 0.1864 | -0.0042 | 0.0507 | -0.0967 | 0.3408 | -0.0445 | -0.0034 | 0.298 | -0.0227 | 0.2705 | -12.3513 | 29.1646 | -18.706 | 10 | 5.3755 | 0.621 | 0.358 | 4.446 | 0.1512 | 4.3926 | -0.3228 | 0.4553 | -0.2788 | -0.3294 | -0.0911 | 1.862 | -0.3761 | -1.8723 | 0.2939 | 0.4067 | 0.0647 | -0.0393 | 0.7673 | -0.0332 | 0.7402 | -31.5618 | 28.1849 | -11.7456 | 11 | 1.742 | -1.4198 | 1.0469 | 2.643 | 0.8265 | 2.4851 | -0.2228 | -0.2642 | 0.2527 | -0.3683 | -0.0109 | 0.9064 | 0.2741 | 0.5086 | 0.3296 | 0.6508 | 0.0155 | -0.0178 | 0.9217 | -0.105 | 0.8211 | -38.1715 | 26.8589 | 1.1925 | 12 | 1.4278 | -1.4705 | -0.1238 | 2.6433 | -1.4844 | 1.0704 | 0.0174 | -0.1591 | 0.1296 | -0.3473 | -0.0589 | -0.0842 | 0.1519 | -0.0756 | 0.1962 | 0.4066 | 0.0236 | -0.0058 | 0.3888 | -0.0168 | 0.4098 | -18.0959 | 31.5896 | -7.3115 | 13 | 3.7343 | 0.3067 | -0.1476 | 2.4891 | 0.2993 | 3.2528 | -0.0589 | -0.0299 | -0.1845 | -0.0177 | -0.0486 | 0.2168 | 0.6036 | -0.1398 | 0.1295 | 0.4792 | -0.0673 | 0.0442 | 0.2837 | 0.0163 | 0.3946 | -25.3619 | 15.7707 | 4.6352 | 14 | 3.0555 | 0.6457 | 2.4735 | 8.2508 | -0.9242 | 4.9161 | 0.1938 | 0.3972 | -1.259 | -0.4465 | 0.5051 | 1.6055 | 2.1377 | -0.8768 | -0.6855 | 0.8407 | -0.1734 | -0.029 | 0.754 | 0.0715 | 0.7395 | -38.2229 | 9.7189 | 11.8918 | 15 | 4.9444 | 0.0538 | -0.5766 | 0.8329 | -0.3003 | 1.5486 | 0.4557 | -0.4978 | 0.8557 | 0.2116 | -0.2399 | -0.1304 | 0.0437 | 0.3012 | -0.2028 | 0.2537 | -0.0052 | -0.0109 | 0.3307 | 0.0015 | 0.3429 | -19.2919 | 18.6269 | 11.5488 | 16 | 3.4619 | 0.5651 | -3.1816 | 2.8646 | -2.266 | 6.418 | 0.4222 | -0.7774 | -0.7227 | 0.3255 | -0.9157 | -0.3196 | -0.784 | 1.2489 | 0.7163 | 0.4218 | -0.0364 | -0.0156 | 0.7754 | 0.0452 | 0.6286 | 1.7449 | 24.1755 | 2.1391 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 2 through 7 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 8 through 13 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 14 through 52 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 53 through 67 )A0 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 68 through 78 )A0 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 79 through 91 )A0 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 92 through 98 )A0 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 99 through 106 )A0 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 107 through 116 )A0 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 117 through 127 )A0 | 11 | X-RAY DIFFRACTION | 11 | chain 'A' and (resid 128 through 132 )A0 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 3 through 25 )B0 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 26 through 98 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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