Software Name Version Classification NB SCALEPACKdata scalingShow PHASER2.3.0phasingShow PHENIX1.7.3_928refinementShow PDB_EXTRACT3.11 data extractionShow Blu-Icedata collection DENZOdata reduction
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 1.902→19.977 Å / Occupancy max : 1 / Occupancy min : 0.8 / SU ML : 0.28 / σ(F) : 0 / Phase error : 38.02 / Stereochemistry target values : MLRfactor Num. reflection % reflection Selection details Rfree 0.3032 2845 5.09 % random Rwork 0.2589 - - - all 0.2611 55872 - - obs 0.2611 55872 97.45 % -
Solvent computation Shrinkage radii : 0.47 Å / VDW probe radii : 0.8 Å / Solvent model : FLAT BULK SOLVENT MODEL / Bsol : 70.052 Å2 / ksol : 0.383 e/Å3 Displacement parameters Biso max : 153.28 Å2 / Biso mean : 46.9088 Å2 / Biso min : 12.95 Å2 Baniso -1 Baniso -2 Baniso -3 1- -5.0568 Å2 0 Å2 0 Å2 2- - 1.8358 Å2 -0 Å2 3- - - 6.8601 Å2
Refinement step Cycle : LAST / Resolution : 1.902→19.977 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 5080 0 6 283 5369
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.009 5198 X-RAY DIFFRACTION f_angle_d1.194 7036 X-RAY DIFFRACTION f_chiral_restr0.079 758 X-RAY DIFFRACTION f_plane_restr0.006 930 X-RAY DIFFRACTION f_dihedral_angle_d16.566 1924
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Number Refine-ID Type Rms dev position (Å)1 1 A2330 X-RAY DIFFRACTION POSITIONAL0.032 1 2 B2330 X-RAY DIFFRACTION POSITIONAL0.032
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 20
Show large table (7 x 20) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)1.9018-1.9345 0.3715 135 0.3206 2611 2746 98 1.9345-1.9697 0.3529 155 0.3285 2627 2782 99 1.9697-2.0075 0.3683 153 0.3045 2670 2823 99 2.0075-2.0485 0.3176 145 0.2899 2675 2820 100 2.0485-2.093 0.35 142 0.2906 2653 2795 99 2.093-2.1416 0.3802 151 0.2862 2646 2797 99 2.1416-2.1951 0.3058 132 0.2766 2678 2810 99 2.1951-2.2544 0.297 140 0.2754 2673 2813 99 2.2544-2.3206 0.3097 150 0.2695 2649 2799 99 2.3206-2.3954 0.2815 144 0.2696 2633 2777 98 2.3954-2.4809 0.3379 124 0.2692 2665 2789 98 2.4809-2.58 0.3293 151 0.2758 2653 2804 97 2.58-2.6971 0.3194 145 0.2664 2598 2743 96 2.6971-2.839 0.3113 154 0.2663 2623 2777 98 2.839-3.0163 0.3463 137 0.2647 2639 2776 97 3.0163-3.2482 0.3388 130 0.262 2617 2747 96 3.2482-3.5735 0.3152 130 0.2626 2631 2761 95 3.5735-4.0867 0.2615 142 0.2384 2644 2786 96 4.0867-5.1343 0.2363 130 0.2171 2656 2786 95 5.1343-19.978 0.2872 155 0.2466 2786 2941 95
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 40) 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 0.1062 -0.1255 0.0728 0.1667 -0.111 0.0854 -0.0166 0.1692 -0.0297 -0.0537 -0.0699 -0.0046 0.0711 -0.0141 -0.2736 0.2564 0.0872 0.0784 0.7436 -0.6401 0.7337 9.9299 -45.3643 23.7987 2 0.005 -0.017 0.0073 0.1148 0.0219 0.4564 0.0971 0.1928 -0.0457 0.1063 0.0576 -0.019 0.0579 0.3036 -0.1714 0.3097 0.0317 -0.0604 0.7075 -0.4568 0.5202 -14.0133 -37.5448 23.4577 3 0.0203 0.0068 -0.0082 0.0305 -0.0183 0.0114 -0.0076 -0.0252 0.0044 0.0185 0.0065 -0.0114 -0.0267 0.005 -0.0284 0.4865 0.0203 -0.1452 0.7932 -0.5319 0.7268 -17.0245 -48.8995 20.6334 4 0.0325 -0.0009 -0.0172 0.0402 -0.0159 0.0665 -0.0116 0.1462 -0.0217 -0.0423 -0.0159 0.0386 -0.0114 0.0933 -0.0933 0.4696 -0.0021 0.065 1.4199 -0.7618 0.7411 -5.4505 -46.9836 11.4245 5 0.1382 -0.0215 -0.1154 0.0971 -0.0523 0.1795 0.0443 0.2827 -0.1804 0.0072 -0.0119 -0.0007 -0.0122 0.1322 -0.0198 0.3493 0.0999 -0.0178 0.5177 -0.6164 0.7105 -4.32 -40.6927 24.4425 6 0.0665 0.0192 -0.0619 0.1258 -0.0386 0.0615 -0.0197 0.0703 -0.042 -0.0169 0.0079 0.0485 0.0549 0.0022 0.0097 0.3547 -0.1236 -0.001 0.6178 -0.555 0.6743 -4.2668 -52.4266 22.1782 7 0.778 0.2664 0.3283 0.1676 0.047 0.1947 -0.0026 0.46 -0.4119 -0.2007 0.4493 -0.3143 0.0656 0.4408 0.9124 0.2464 -0.0025 -0.0437 0.3571 -0.2503 0.331 -6.8576 -34.0652 30.0668 8 0.0761 -0.0258 0.022 0.0085 -0.0067 0.0064 0.1067 0.0054 0.0697 -0.0612 0.0852 -0.0328 -0.0925 0.0523 0.0263 0.3012 0.0585 -0.0332 0.2279 -0.1025 0.3451 -11.4526 -26.3298 45.8754 9 0.1341 0.0035 0.0216 0.0091 0.0251 0.0355 -0.0803 0.1394 -0.1879 -0.0686 0.0143 -0.087 -0.0572 0.0264 -0.1962 0.1674 0.0472 0.0164 0.0735 -0.2859 0.3228 -0.9814 -34.0958 42.6251 10 0.5479 0.1522 0.0795 0.0703 0.0822 0.1313 -0.1534 0.3259 0.0487 -0.1241 0.0423 0.1387 -0.1424 -0.1949 -0.1045 0.2488 -0.0038 0.05 0.3544 -0.2019 0.4539 -1.264 -38.7235 32.9402 11 0.0081 0.0115 -0.0064 0.0359 -0.0153 0.0079 0.0264 0.0222 0.11 -0.1012 0.1446 0.0674 -0.0541 -0.0074 -0.0003 0.2964 0.0156 -0.112 0.3521 0.0422 0.6284 -6.4173 -16.662 32.326 12 0.1372 -0.1001 0.151 0.1575 -0.1621 0.1905 0.0645 0.1548 -0.017 -0.2518 -0.066 0.025 -0.18 0.0655 -0.2652 0.1865 0.0009 -0.0112 0.3849 -0.1009 -0.1215 3.0543 -28.3642 37.0918 13 0.0988 0.0578 -0.0318 0.0763 -0.0685 0.1637 0.1214 0.8655 0.2368 -0.098 0.0214 -0.0111 0.0963 -0.0933 0.0338 0.3432 -0.0003 -0.0138 0.623 0.1009 0.6771 3.5835 -20.7802 24.6795 14 0.0788 0.0226 0.0113 0.0532 0.0256 0.0197 0.1386 0.2696 -0.131 -0.0582 -0.0502 0.2178 -0.0169 -0.148 0.0791 0.2488 -0.0419 -0.0141 1.1517 0.0276 0.9229 0.3888 -23.1635 17.1568 15 0.0011 -0.0009 -0.0009 0.0022 0.0042 0.0074 0.0427 0.0206 0.0406 -0.0546 0.0389 0.0798 -0.0704 0.0863 0.0004 0.7279 0.1404 -0.1563 1.5353 0.0637 0.689 -1.6234 -20.5666 6.9656 16 0.0649 0.0347 0.1131 0.0796 -0.0122 0.3389 -0.0568 0.1019 0.0715 -0.0694 0.0964 0.0096 0.0251 -0.0208 -0.0063 0.403 0.0024 -0.0079 1.3256 -0.1296 0.7775 11.289 -22.9327 11.7186 17 0.0674 -0.0927 0.0572 0.4202 -0.369 0.341 0.0547 0.2326 -0.0523 -0.1112 -0.2011 0.0977 0.0705 0.2674 -0.1932 0.4899 0.0354 0.0418 1.1139 -0.4455 0.7072 -15.3441 -33.3487 14.8829 18 0.0462 0.1051 0.1406 0.2672 0.341 0.4563 -0.072 0.2029 0.0152 -0.1117 0.0988 0.0448 -0.0339 0.1685 0.0327 0.4621 0.0694 -0.0388 1.8176 -0.2997 0.8795 -5.2649 -32.0604 5.5293 19 0.0032 0.0037 0.0052 0.0046 0.0084 0.017 -0.1026 0.0052 -0.0409 -0.0119 -0.1085 -0.0062 0.0292 0.0096 -0.0003 0.8725 0.0601 -0.078 1.4401 -0.2668 0.7583 11.6446 -29.2702 0.8437 20 0.0014 0.0038 -0.0035 0.2141 0.0225 0.2928 0.0118 0.1369 -0.0062 0.0094 0.0347 0.0314 -0.0073 -0.1322 0.19 0.4543 0.1414 -0.0836 1.0449 -0.3399 0.4828 12.0557 -34.4835 15.7281 21 0.0397 0.0718 0.0386 0.1431 0.0609 0.0441 -0.0585 0.1426 -0.2513 -0.1413 0.0443 0.0354 0.0672 -0.0227 0.0392 0.1128 0.0577 0.1702 -0.089 -0.4591 0.6178 -44.9136 -45.3356 43.6157 22 0.0196 -0.0098 0.0244 0.03 -0.0131 0.0435 -0.0029 0.1801 -0.0831 -0.2089 0.037 -0.3637 0.0533 0.2842 0.0258 0.1206 0.1064 0.1542 -0.2419 -0.3745 0.098 -20.9682 -37.5231 43.9505 23 0.0379 -0.0245 -0.0077 0.0152 0.0053 0.0014 -0.0394 0.0084 -0.0045 0.0258 -0.0571 0.0016 -0.0381 0.0131 -0.0401 0.3981 -0.0405 0.0491 0.1419 -0.0115 0.9832 -17.9587 -48.8549 46.789 24 0.0617 -0.0058 0.0418 0.0073 -0.0038 0.0328 0.0582 0.0114 -0.141 -0.0309 0.0683 -0.1396 -0.0512 -0.0243 0.0041 0.2485 0.022 0.0362 0.204 0.0535 0.4276 -29.5298 -46.9252 55.9924 25 0.2086 0.0125 -0.0449 0.1013 0.1218 0.1299 -0.0399 0.2537 -0.2216 -0.2311 -0.0423 -0.115 -0.2046 0.052 -0.1392 0.1517 -0.0112 0.0692 -0.1816 -0.2593 0.1089 -30.6661 -40.6586 42.9694 26 0.0529 -0.0346 -0.0298 0.0507 0.054 0.0602 -0.0062 0.0017 -0.0577 -0.0425 0.042 -0.0316 0.0556 0.0271 0.0741 0.3573 -0.0477 0.2478 0.0823 -0.072 0.6358 -30.7162 -52.3783 45.2483 27 0.1134 0.0624 0.099 0.2889 0.0141 0.0929 -0.1491 0.2308 -0.0172 -0.1269 0.0164 -0.1482 0.0077 0.0647 -0.1629 0.2211 -0.0075 0.0429 -0.004 -0.1948 0.5692 -28.1316 -34.0459 37.34 28 0.0206 0.0045 0.0106 0.0016 0.0014 0.0056 0.1321 0.0303 0.0575 0.0486 0.0484 0.054 -0.056 -0.0022 0.0018 0.4476 -0.0255 0.098 0.6836 -0.0779 0.5284 -23.5339 -26.3243 21.5144 29 0.1187 0.0551 0.2918 0.0287 0.1436 0.7284 -0.0198 0.3728 -0.0018 -0.0968 -0.0937 0.1331 -0.2009 0.0204 -0.2452 0.2789 0.0022 -0.0163 0.5441 -0.2471 0.5249 -34.0032 -34.0895 24.7697 30 0.0921 0.0243 -0.0235 0.2178 -0.1653 0.1245 0.054 0.2087 -0.3667 0.0911 -0.0264 -0.0073 -0.0119 0.0613 0.2248 0.1696 -0.0466 -0.0297 0.193 -0.2151 0.5003 -33.7244 -38.7025 34.4679 31 0.0305 -0.0232 0.0228 0.0274 -0.0004 0.0599 -0.0011 0.0479 0.0476 0.0475 -0.0041 -0.031 -0.0481 -0.0132 -0.0061 0.2651 -0.1077 -0.041 0.2737 0.1483 0.3414 -28.5695 -16.6438 35.0514 32 0.0778 0.0186 0.0579 0.0075 0.0039 0.2076 -0.2183 0.345 0.0062 -0.1131 -0.2946 -0.1637 -0.1692 0.0038 -0.1031 0.2953 -0.0164 -0.0152 0.3046 0.0033 0.7423 -38.0394 -28.3517 30.3019 33 1.8061 -0.146 -0.1854 0.5757 -0.3978 0.3299 0.0088 0.6258 -0.0687 -0.3355 0.0133 0.169 0.2572 -0.0982 0.3661 0.0837 -0.016 0.024 0.0885 0.0683 0.038 -38.5722 -20.7562 42.7038 34 0.5371 0.1262 -0.4981 0.3371 -0.1546 0.8727 0.1305 0.2071 0.132 -0.1438 -0.025 0.0923 -0.147 -0.2037 0.2485 0.1144 0.0009 0.0325 -0.0029 0.129 -0.2175 -35.3773 -23.1652 50.226 35 0.2685 -0.1298 -0.0321 0.0734 0.0219 0.008 0.0832 -0.1758 0.1166 0.0318 0.0358 -0.1283 -0.0981 -0.0716 0.0435 0.4242 0.0092 -0.0106 0.2205 -0.0727 0.1984 -33.3643 -20.5116 60.4167 36 0.0895 0.0349 0.0085 0.0386 0.029 0.0303 0.0266 0.0885 -0.0543 -0.1034 0.1565 -0.0428 0.1399 0.0108 0.1087 0.2917 0.0605 0.0576 0.2374 -0.0085 0.1156 -46.276 -22.8876 55.6674 37 0.1275 0.0581 0.0059 0.0672 0.0298 0.1337 -0.0272 -0.0382 -0.0643 0.0178 0.0356 -0.0539 0.08 -0.0298 0.061 0.1276 0.0062 -0.0285 0.1614 -0.0304 0.0822 -19.6914 -33.4671 52.4625 38 0.0465 -0.0567 -0.0484 0.2615 0.1421 0.0931 0.0008 -0.2626 -0.0161 0.1965 0.1368 -0.0712 -0.1127 -0.0331 0.1814 0.1849 -0.0161 -0.0196 0.2629 0.044 0.0048 -29.7099 -32.0104 61.8754 39 0.0654 -0.0179 0.0669 0.1025 -0.0462 0.0753 -0.022 0.0538 -0.0833 -0.0341 -0.0473 0.0296 0.0609 -0.0606 -0.1588 0.3677 0.0046 0.1772 0.3495 -0.0212 0.1018 -46.6319 -29.2042 66.5486 40 0.1585 -0.4179 0.0344 1.1444 -0.0724 0.037 0.0301 0.1702 -0.2285 -0.2012 -0.0432 0.1159 0.0469 -0.0354 0.0339 0.1502 -0.0202 0.0965 0.0402 -0.0578 0.4661 -47.0417 -34.4389 51.6775
Refinement TLS group Show large table (6 x 40) Hide large table ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 (chain A and resid 3:19)A3 - 19 2 X-RAY DIFFRACTION 2 (chain A and resid 20:41)A20 - 41 3 X-RAY DIFFRACTION 3 (chain A and resid 42:47)A42 - 47 4 X-RAY DIFFRACTION 4 (chain A and resid 48:61)A48 - 61 5 X-RAY DIFFRACTION 5 (chain A and resid 62:81)A62 - 81 6 X-RAY DIFFRACTION 6 (chain A and resid 82:87)A82 - 87 7 X-RAY DIFFRACTION 7 (chain A and resid 88:109)A88 - 109 8 X-RAY DIFFRACTION 8 (chain A and resid 110:114)A110 - 114 9 X-RAY DIFFRACTION 9 (chain A and resid 115:131)A115 - 131 10 X-RAY DIFFRACTION 10 (chain A and resid 132:149)A132 - 149 11 X-RAY DIFFRACTION 11 (chain A and resid 150:155)A150 - 155 12 X-RAY DIFFRACTION 12 (chain A and resid 156:175)A156 - 175 13 X-RAY DIFFRACTION 13 (chain A and resid 176:217)A176 - 217 14 X-RAY DIFFRACTION 14 (chain A and resid 218:240)A218 - 240 15 X-RAY DIFFRACTION 15 (chain A and