Software Name Version Classification PHENIX1.12_2829refinement CrystalCleardata collection SCALAdata scaling PDB_EXTRACT3.22 data extraction iMOSFLMdata reduction PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 4GSZ, 3SKJResolution : 2.49→30.713 Å / SU ML : 0.38 / Cross valid method : FREE R-VALUE / σ(F) : 1.34 / Phase error : 26.52 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.2618 1992 6.09 % Rwork 0.2057 30720 - obs 0.209 32712 99.75 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso max : 123.34 Å2 / Biso mean : 45.2615 Å2 / Biso min : 10.37 Å2 Refinement step Cycle : final / Resolution : 2.49→30.713 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 6336 0 18 309 6663 Biso mean - - 48.31 33.74 - Num. residues - - - - 837
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.003 6488 X-RAY DIFFRACTION f_angle_d0.473 8826 X-RAY DIFFRACTION f_chiral_restr0.04 1005 X-RAY DIFFRACTION f_plane_restr0.003 1125 X-RAY DIFFRACTION f_dihedral_angle_d14.621 3872
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Rfactor Rfree error : 0 / Total num. of bins used : 14
Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)2.49-2.5523 0.4176 137 0.3023 2138 2275 98 2.5523-2.6212 0.3425 143 0.2881 2179 2322 100 2.6212-2.6983 0.3494 143 0.2619 2178 2321 100 2.6983-2.7854 0.2928 146 0.2575 2204 2350 100 2.7854-2.8848 0.3113 143 0.253 2162 2305 100 2.8848-3.0003 0.3242 142 0.2397 2168 2310 100 3.0003-3.1367 0.323 138 0.2499 2218 2356 100 3.1367-3.3019 0.2713 144 0.2227 2193 2337 100 3.3019-3.5085 0.2741 140 0.2079 2202 2342 100 3.5085-3.7789 0.267 140 0.2073 2191 2331 100 3.7789-4.1584 0.2586 138 0.1845 2195 2333 100 4.1584-4.7582 0.2052 144 0.1534 2215 2359 100 4.7582-5.9875 0.1889 142 0.1563 2222 2364 100 5.9875-30.7156 0.2061 152 0.178 2255 2407 100
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 32) Hide large table 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)1 3.9021 -0.342 -2.2455 4.1044 -0.3376 1.3572 0.1794 -0.3385 -0.0252 0.5992 -0.0816 -0.3322 0.1843 0.8252 -0.1117 0.1714 -0.0254 -0.0259 0.3463 0.0784 0.334 106.97 81.9776 119.9271 2 2.7266 -0.1319 0.8807 3.2573 1.9147 7.3785 0.0957 -0.0014 0.2525 -0.026 0.0175 -0.7592 -0.217 1.0696 -0.0406 0.2071 -0.0273 -0.0911 0.4246 0.0457 0.4389 108.1906 85.0426 110.9935 3 4.2891 0.8908 -0.3064 4.6187 0.0182 4.688 -0.412 0.4092 0.8043 0.199 0.0592 -0.4662 -0.7324 0.2143 0.2362 0.3618 -0.1125 -0.0853 0.3233 0.0357 0.524 105.663 95.7661 115.5759 4 6.5337 1.6163 0.6961 8.4679 4.3486 7.2448 0.0567 -0.5327 0.0677 0.4179 -0.1085 -0.5461 -0.2515 1.4016 -0.1449 0.1737 -0.0511 -0.1003 0.514 0.0524 0.3804 113.723 86.7097 114.0324 5 2.2818 -1.5127 -1.9356 3.5425 -0.976 4.1426 0.1366 -0.3205 -0.0889 0.4492 -0.0214 -1.0682 -1.4341 0.3382 -0.237 0.3428 -0.1518 -0.0714 0.4493 -0.0543 0.4892 105.1974 90.3378 121.7135 6 2.1695 0.352 -0.1394 0.6632 -2.3487 8.729 0.1978 0.0212 0.2051 0.0653 -0.0587 -0.0559 0.0734 0.7158 -0.1673 0.205 0.0256 -0.0512 0.1233 -0.026 0.3292 101.4984 83.0133 120.127 7 2.0328 -0.48 1.9357 3.3755 1.8228 4.6557 -0.414 -0.3801 0.0532 0.5866 0.5347 1.4252 -0.0675 -0.9879 -0.1086 0.4411 0.125 0.1737 0.6626 0.3025 0.707 72.7326 72.6949 138.2368 8 6.9994 4.9693 -0.2229 6.1714 0.1271 3.5995 -0.1876 -0.2535 -0.1309 0.3304 0.3413 -0.1644 0.3794 -0.0926 -0.1536 0.3099 0.1217 0.0416 0.3088 0.0489 0.1736 87.6958 71.519 135.1269 9 3.7586 3.1948 -0.2548 7.2896 -1.8759 1.9147 -0.2449 -0.0881 0.0555 0.1754 0.5367 -0.0116 -0.0282 0.1289 -0.2551 0.3309 0.0862 0.009 0.3172 -0.0511 0.1831 88.5016 74.8564 132.6627 10 2.5557 0.6628 -1.4101 4.2662 -2.0249 3.9483 -0.0934 -0.0838 -0.1132 0.2031 0.5445 0.6824 0.2346 -0.6518 -0.5349 0.4036 0.1051 0.0359 0.4086 0.1164 0.3012 81.2263 65.2168 137.8024 11 4.5378 2.0311 -3.0082 2.9535 -0.4453 2.8711 -0.0911 -0.1026 0.2326 0.7272 0.3138 0.2804 -0.1298 0.1679 -0.3387 0.4564 0.1868 0.1205 0.387 0.0838 0.2595 93.3816 56.2494 146.2788 12 5.0203 0.0272 -1.5567 0.9022 0.3596 0.7438 0.1678 -0.3598 0.4108 0.3327 0.2766 0.2122 0.1177 -0.3757 -0.4178 0.7739 0.174 0.1753 0.64 0.3177 0.4194 86.4634 50.9182 150.1668 13 8.1484 -2.0984 3.2808 4.3701 -0.6847 4.9287 -0.2609 -0.765 -1.1984 0.4739 -0.1508 0.2484 0.5457 0.2387 0.046 0.6596 0.0921 0.0602 0.3972 0.1219 0.2944 95.0319 42.3845 151.1765 14 4.8533 0.7657 0.8205 3.3119 0.0287 5.5693 -0.1994 -0.754 0.034 0.7482 0.1165 0.3106 0.2883 -0.0734 0.0456 0.6405 0.1478 0.1316 0.4561 0.1651 0.3248 90.8772 49.6555 149.3034 15 7.8554 7.4798 -4.1091 9.099 -4.1783 2.1815 -0.3131 -0.372 0.256 -0.0348 0.126 -0.1591 -0.2812 0.1075 0.0313 0.3453 0.0417 -0.0784 0.4712 -0.0499 0.2171 107.4634 59.8281 138.3584 16 5.0268 1.7779 5.4898 5.015 2.631 6.7091 0.2443 0.2866 -0.4248 -0.5681 0.1764 -0.2211 0.8889 0.3234 -0.2139 0.3527 -0.0921 0.0257 0.2583 -0.0486 0.3368 105.5807 56.8554 108.47 17 3.4472 0.3581 2.3774 2.1723 -0.0303 2.9346 -0.1839 -0.0531 0.0698 0.4512 0.373 0.2034 -0.0362 -0.0989 -0.1457 0.2509 0.0284 -0.0208 0.2364 0.0138 0.2592 103.1665 62.5767 122.4395 18 1.0134 0.668 0.4989 4.0477 -2.4827 5.9907 0.3046 0.0238 -0.171 0.3275 0.1836 0.2635 0.3726 0.1617 -0.391 0.2517 0.0336 -0.0235 0.2138 -0.0561 0.2963 102.3143 59.2408 124.9666 19 1.5256 0.5471 0.5659 2.6292 -0.3908 6.6379 -0.2487 0.29 0.1379 -0.3082 0.0192 0.1621 0.4325 -0.5161 -0.1028 0.1692 -0.0504 -0.0344 0.2539 0.0304 0.2996 98.0203 61.0655 108.3149 20 2.0125 -0.0653 2.5734 4.2177 -0.7476 5.5697 -0.0001 0.3268 0.2658 -0.0639 0.0485 -0.0459 -0.3121 0.8255 0.0716 0.1467 -0.0162 0.0299 0.2912 0.0528 0.3604 106.3056 69.2372 115.5245 21 4.7331 1.413 -1.0215 7.0017 -1.725 6.0039 -0.0773 -0.7441 0.8057 0.0044 0.1729 0.3785 -0.1418 -0.7563 -0.1074 0.1689 0.0754 -0.0294 0.2024 0.0084 0.3056 81.1002 93.4857 107.5683 22 2.4338 1.8268 -1.2502 4.8862 -1.1107 3.65 0.2278 -0.283 0.8259 0.2273 -0.2715 -0.4055 -0.1983 0.3729 0.0112 0.2176 -0.021 0.0215 0.1648 0.0547 0.5441 90.6737 95.7447 104.905 23 2.9752 0.2116 0.4254 6.043 -0.6545 3.9312 -0.1349 0.2174 0.1779 -0.4838 0.0715 -0.0067 0.0264 -0.0438 0.0556 0.1882 0.0156 -0.0199 0.2483 0.14 0.4396 89.3751 92.8648 97.1349 24 6.4823 2.7107 1.2776 1.9653 -1.1792 3.9423 -0.007 -0.2915 -0.4221 -0.1563 -0.1002 -0.989 0.0759 0.1121 0.113 0.228 0.0527 -0.0333 0.1762 0.0384 0.4845 86.4572 87.7352 105.918 25 2.524 -1.1233 -1.0263 1.8388 -1.9089 4.3893 0.3719 -0.1298 0.2321 0.3344 -0.2713 -0.2508 -0.739 0.0984 -0.1357 0.2347 -0.0936 -0.0026 0.2846 -0.0335 0.3294 85.662 90.8321 111.5808 26 6.6691 0.907 0.9099 5.7498 0.8003 1.9269 0.3187 -1.2897 0.0895 0.7668 0.5814 0.6574 -0.0383 -0.4331 -0.0303 0.4179 0.2711 0.1379 0.5477 0.1356 0.4186 76.1017 78.2891 140.5509 27 3.8207 0.7986 -0.0916 1.6797 -0.6817 2.6118 -0.0719 -0.1889 0.9345 0.7054 0.3938 0.502 -0.4013 -0.3695 0.0766 0.3913 0.1831 0.075 0.2449 0.0735 0.5291 75.4448 87.8711 129.6172 28 3.3981 0.0761 -0.3238 2.2679 -0.5402 3.7654 -0.0461 -0.7496 0.4136 0.5217 0.3549 0.0148 -0.2045 -0.2377 -0.2022 0.3371 0.1496 0.0009 0.3667 -0.0364 0.2999 79.9105 83.0251 134.8842 29 2.9891 -0.1816 2.2395 0.8757 0.7351 2.8043 -0.4412 -0.2899 1.0897 0.6018 0.4255 -0.1565 -1.5453 -1.0326 0.3347 0.5955 0.2979 0.1144 0.5826 0.1334 0.6699 70.1302 89.3126 133.2794 30 3.6029 0.59 0.2499 1.0677 -0.4249 2.2302 -0.2244 -0.0156 -1.1345 0.3238 0.3652 0.7722 1.558 -0.7669 -0.2161 1.1457 -0.3037 0.3728 0.4754 0.3248 0.9107 82.4341 33.0502 137.5724 31 1.3395 -0.6852 -0.3063 2.0679 -0.5674 3.828 -0.1263 0.133 -0.1447 0.2395 0.4946 0.6073 0.9457 -0.9041 -0.3382 0.56 -0.1192 0.0215 0.3303 0.0531 0.4127 91.4291 41.3195 125.8467 32 5.5422 1.9616 0.0558 2.6711 0.9484 1.446 -0.1346 0.2475 -0.6112 -0.3001 0.1448 -0.3815 0.258 0.0736 -0.05 0.3551 0.039 -0.0202 0.1893 -0.0213 0.2467 108.0444 46.1299 116.1066
Refinement TLS group Show large table (6 x 32) Hide large table ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain 'L' and (resid 1 through 18 )L1 - 18 2 X-RAY DIFFRACTION 2 chain 'L' and (resid 19 through 38 )L19 - 38 3 X-RAY DIFFRACTION 3 chain 'L' and (resid 39 through 61 )L39 - 61 4 X-RAY DIFFRACTION 4 chain 'L' and (resid 62 through 75 )L62 - 75 5 X-RAY DIFFRACTION 5 chain 'L' and (resid 76 through 90 )L76 - 90 6 X-RAY DIFFRACTION 6 chain 'L' and (resid 91 through 113 )L91 - 113 7 X-RAY DIFFRACTION 7 chain 'L' and (resid 114 through 128 )L114 - 128 8 X-RAY DIFFRACTION 8 chain 'L' and (resid 129 through 150 )L129 - 150 9 X-RAY DIFFRACTION 9 chain 'L' and (resid 151 through 174 )L151 - 174 10 X-RAY DIFFRACTION 10 chain 'L' and (resid 175 through 211 )L175 - 211 11 X-RAY DIFFRACTION 11 chain 'A' and (resid 1 through 18 )A1 - 18 12 X-RAY DIFFRACTION 12 chain 'A' and (resid 19 through 38 )A19 - 38 13 X-RAY DIFFRACTION 13 chain 'A' and (resid 39 through 61 )A