Software Name Version Classification SBC-Collectdata collection HKL-3000data collection HKL-3000phasing MOLREPphasing PHENIX(phenix.refine: dev_1745)refinement HKL-3000data reduction HKL-3000data scaling
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : PDBID 1OG6Resolution : 1.949→37.391 Å / SU ML : 0.26 / Isotropic thermal model : mixed / Cross valid method : THROUGHOUT / σ(F) : 0 / Phase error : 24.77 / Stereochemistry target values : MLRfactor Num. reflection % reflection Selection details Rfree 0.228 3331 5.07 % random Rwork 0.186 - - - obs 0.188 65745 96.53 % - all - 65745 - -
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso mean : 37.4 Å2 Refinement step Cycle : LAST / Resolution : 1.949→37.391 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 7021 0 0 243 7264
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.007 7419 X-RAY DIFFRACTION f_angle_d1.061 10093 X-RAY DIFFRACTION f_dihedral_angle_d15.158 2768 X-RAY DIFFRACTION f_chiral_restr0.04 1126 X-RAY DIFFRACTION f_plane_restr0.005 1318
LS refinement shell Refine-ID : X-RAY DIFFRACTION
Show large table (7 x 24) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection obs % reflection obs (%)1.9487-1.9765 0.3015 123 0.2644 2296 2419 85 1.9765-2.006 0.2909 154 0.2627 2517 2671 95 2.006-2.0373 0.3342 132 0.2549 2599 2731 97 2.0373-2.0707 0.2959 130 0.2447 2660 2790 98 2.0707-2.1064 0.2642 140 0.2326 2580 2720 98 2.1064-2.1447 0.2568 131 0.226 2636 2767 98 2.1447-2.186 0.2951 143 0.2264 2632 2775 98 2.186-2.2306 0.3118 130 0.2276 2643 2773 98 2.2306-2.2791 0.2862 152 0.2142 2605 2757 98 2.2791-2.3321 0.2677 144 0.2074 2623 2767 98 2.3321-2.3904 0.2637 141 0.2019 2630 2771 98 2.3904-2.455 0.2513 143 0.2034 2614 2757 98 2.455-2.5273 0.2577 149 0.2104 2607 2756 98 2.5273-2.6088 0.254 141 0.2115 2621 2862 98 2.6088-2.702 0.2852 136 0.2134 2659 2795 98 2.702-2.8102 0.2709 161 0.214 2607 2768 98 2.8102-2.938 0.2415 140 0.1935 2627 2767 98 2.938-3.0929 0.2159 141 0.1973 2649 2790 98 3.0929-3.2865 0.2867 125 0.2022 2621 2746 97 3.2865-3.5401 0.2158 141 0.1821 2657 2790 98 3.5401-3.896 0.1951 119 0.1565 2629 2748 96 3.896-4.459 0.1705 133 0.15 2606 2739 96 4.459-5.6148 0.1744 130 0.1429 2573 2703 94 5.6148-37.3974 0.1842 152 0.1609 2523 2775 91
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 26) 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 1.843 0.4694 0.2674 1.7331 0.4279 1.0364 -0.0585 0.0472 -0.0681 -0.0356 0.0186 0.1342 0.1266 -0.2521 0.0312 0.2368 -0.0459 -0.0022 0.3331 -0.0351 0.2677 -32.2606 -46.0531 19.2154 2 1.7639 1.2579 -0.299 2.9196 -0.835 2.2008 0.0204 -0.1861 0.2213 -0.0195 -0.0273 0.1611 -0.0656 -0.2495 -0.0089 0.1892 0.0434 0.0041 0.262 -0.0235 0.1978 -27.7559 -28.1443 18.8509 3 5.188 0.4683 -2.2738 2.2394 -0.3463 2.6613 -0.0251 -0.3685 0.4473 0.2356 0.0874 0.0565 -0.0085 -0.1319 -0.0319 0.2546 0.0178 -0.0348 0.3216 -0.0232 0.2118 -22.5241 -30.6967 28.713 4 0.3896 -0.3263 -0.064 1.8124 0.8456 0.7757 0.0354 -0.0028 -0.0237 -0.165 -0.0315 -0.0978 -0.07 -0.1297 -0.002 0.218 -0.0101 -0.0138 0.246 0.018 0.2895 -12.7306 -41.1527 17.1942 5 4.7902 0.8305 1.8098 2.7538 2.6038 6.7217 0.1663 0.342 -0.6724 -0.2856 0.0839 -0.2203 0.1241 -0.0807 -0.2509 0.3484 0.0029 0.0448 0.2635 -0.0375 0.3291 -14.5763 -57.9379 3.142 6 5.2938 -1.348 -0.0432 3.1052 -0.7466 1.7382 -0.2795 0.3351 -0.6729 -0.3436 0.1664 0.4678 0.4467 -0.3125 0.0574 0.4036 -0.1131 0.0525 0.3395 -0.0363 0.3727 -21.6732 -55.167 14.8829 7 6.4447 -2.7458 1.4078 1.17 -0.7662 8.3526 -0.2026 0.3595 -0.2454 0.1422 -0.3078 -0.2315 0.3661 0.3404 0.4497 0.339 -0.0048 -0.0001 0.2244 -0.06 0.3685 -5.5614 -57.6804 8.8431 8 2.8893 0.5009 0.0343 2.47 -0.8294 1.7452 -0.0121 0.051 -0.1568 -0.1795 0.1464 0.2751 0.2405 -0.2955 -0.1397 0.297 -0.092 -0.0095 0.3401 -0.0045 0.3322 -26.9986 -53.6437 -20.0496 9 3.2093 -0.0697 0.47 1.6199 -0.3611 2.3683 -0.0534 0.1416 -0.3675 -0.2143 0.027 0.0039 0.3546 0.025 0.0281 0.3491 -0.0253 0.0134 0.2006 -0.0176 0.3245 -9.5655 -59.0106 -19.3433 10 3.9864 1.1093 0.9686 4.013 0.7086 3.9176 -0.0422 0.521 -0.2206 -0.4542 0.0448 -0.4036 0.4659 0.0441 -0.0358 0.353 -0.0048 0.0518 0.2558 0.006 0.1815 -9.0228 -53.1501 -29.1332 11 1.5405 -0.5174 -0.6704 0.3867 0.4314 1.7376 -0.0846 -0.1092 0.1303 0.1284 0.1153 0.0335 0.2149 -0.0824 -0.0592 0.2629 -0.0097 0.0082 0.2416 0.021 0.3216 -13.389 -39.5127 -17.441 12 2.7404 -1.4796 0.9781 4.1515 -1.1013 4.4499 0.0132 -0.2874 1.0723 0.5063 0.033 0.3648 -0.0776 -0.4243 -0.0593 0.302 0.0149 0.0112 0.342 -0.0818 0.5788 -27.8938 -32.2501 0.9851 13 4.3875 -1.3642 -1.711 5.4816 1.4 4.8756 -0.0303 -0.1687 -0.565 -0.3963 -0.0336 0.9785 -0.1131 -0.3891 0.0066 0.2365 -0.0002 -0.0422 0.3547 0.0677 0.4158 -30.726 -33.9588 -10.296 14 1.5553 -0.3788 0.3544 5.3156 0.5711 1.5318 0.0632 -0.2529 -0.127 0.3338 -0.1769 0.6495 -0.1106 -0.4054 0.0821 0.2661 -0.0166 0.01 0.4339 -0.0438 0.3725 -30.0528 -40.3773 -15.3656 15 0.6452 -0.4743 -1.4995 7.7397 -0.7055 6.118 0.0229 -0.0503 0.2325 0.3483 -0.2537 0.1796 -0.5733 0.0455 0.1362 0.2287 0.0126 0.0344 0.3307 0.0251 0.3476 -24.3897 -25.219 -9.458 16 1.5926 1.5493 0.1728 2.2514 0.3996 0.4175 0.1269 0.7645 0.0446 -0.5433 0.5372 -0.5558 -0.2449 0.3983 -0.5438 0.4109 -0.0088 0.0429 0.3641 -0.0285 0.4817 4.05 -7.2893 -29.6662 17 2.3144 -0.5385 0.1255 3.2015 0.0399 1.4412 0.0528 0.0166 0.3562 0.1516 -0.0401 -0.186 -0.38 0.0122 -0.0154 0.3872 0.0152 -0.0189 0.235 0.0001 0.3759 -3.4627 3.646 -15.5683 18 2.8415 0.3064 -0.2226 3.3098 -0.361 1.369 0.0144 0.1836 0.4856 -0.2479 -0.0057 0.1417 -0.3074 -0.271 -0.0347 0.3979 0.0654 -0.0232 0.2689 0.0232 0.4042 -10.3077 2.6294 -20.8447 19 1.532 0.8617 -1.4438 2.4534 0.2823 2.8041 0.002 0.0989 0.2261 -0.1117 -0.0073 0.3719 -0.0437 -0.3659 -0.014 0.2523 0.0988 -0.0194 0.3257 0.0183 0.3915 -21.0859 -10.8983 -17.2796 20 2.7281 1.9088 -1.1086 5.7251 -0.7419 1.8509 -0.0924 -0.0176 0.1672 -0.4455 0.1176 -0.0108 0.0033 -0.1367 -0.0327 0.2288 0.0364 -0.0059 0.2554 0.0005 0.2916 -12.2901 -11.6216 -22.6102 21 3.4229 -0.0696 -0.7536 5.0917 -0.9908 3.4013 -0.0554 0.3886 0.0038 -0.3548 0.184 0.3411 -0.2942 -0.3861 -0.1685 0.2682 0.0249 -0.0048 0.2843 0.0035 0.2255 -12.8349 -14.4977 -29.0596 22 1.7806 1.0248 0.5171 1.2585 0.4647 1.6364 0.0672 -0.0595 0.1363 0.135 -0.0186 -0.2049 -0.0976 0.0178 -0.0245 0.2649 0.021 0.0035 0.2103 -0.0267 0.3507 0.6094 -19.1628 -20.2836 23 2.9957 0.9073 0.1707 1.8499 0.1772 3.6187 0.3082 -0.2218 -0.489 0.3314 -0.0935 -0.5335 -0.1699 -0.122 -0.1771 0.3568 -0.0193 -0.0602 0.3459 0.025 0.4282 12.2065 -8.5916 0.8216 24 3.3569 -0.6221 0.675 1.5672 -0.2862 2.6575 0.0676 -0.1695 0.697 -0.0804 -0.1158 -0.0704 -0.4373 -0.0002 0.0457 0.3249 -0.0192 0.0153 0.2382 -0.0262 0.4127 10.5336 -6.7614 -12.9502 25 5.8269 -2.361 0.2078 2.2965 -1.2573 2.5148 0.1692 0.3269 1.2377 -0.0101 0.08 -0.6857 -0.674 0.1842 -0.2249 0.584 -0.1362 -0.0557 0.3816 0.0785 0.7741 12.942 -0.0967 -13.5609 26 3.1383 -0.8545 -5.313 0.7507 0.8612 9.7617 -0.322 -0.3665 -1.5252 0.0242 -0.4005 -0.4294 -0.0222 0.2456 0.6018 0.2827 -0.0323 -0.0136 0.327 0.0211 0.5074 18.0525 -18.3103 -6.5892
Refinement TLS group Show large table (4 x 26) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 1 through 84 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 85 through 135 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 136 through 161 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 162 through 220 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 221 through 251 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 252 through 277 )7 X-RAY DIFFRACTION 7 chain 'A' and (resid 278 through 293 )8 X-RAY DIFFRACTION 8 chain 'B' and (resid 1 through 84 )9 X-RAY DIFFRACTION 9 chain 'B' and (resid 85 through 135 )10 X-RAY DIFFRACTION 10 chain 'B' and (resid 136 through 161 )11 X-RAY DIFFRACTION 11 chain 'B' and (resid 162 through 220 )12 X-RAY DIFFRACTION 12 chain 'B' and (resid 221 through 236 )13 X-RAY DIFFRACTION 13 chain 'B' and (resid 237 through 251 )14 X-RAY DIFFRACTION 14 chain 'B' and (resid 252 through 277 )15 X-RAY DIFFRACTION 15 chain 'B' and (resid 278 through 293 )16 X-RAY DIFFRACTION 16 chain 'C'