Software Name Version Classification PHENIX1.10.1_2155refinement XDSdata reduction XSCALEdata scaling SHARPphasing
Refinement Method to determine structure : SIRAS / Resolution : 2.4→24.961 Å / SU ML : 0.3 / Cross valid method : THROUGHOUT / Phase error : 20.81 Rfactor Num. reflection % reflection Selection details Rfree 0.2149 5887 5 % Random Rwork 0.1829 - - - obs 0.1845 117755 99.91 % -
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 ÅRefinement step Cycle : LAST / Resolution : 2.4→24.961 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 9700 0 106 508 10314
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.008 10117 X-RAY DIFFRACTION f_angle_d0.956 13747 X-RAY DIFFRACTION f_dihedral_angle_d13.493 5985 X-RAY DIFFRACTION f_chiral_restr0.056 1444 X-RAY DIFFRACTION f_plane_restr0.007 1742
LS refinement shell Show large table (7 x 30) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.4-2.4273 0.3517 188 0.3124 3576 X-RAY DIFFRACTION 98 2.4273-2.4558 0.3038 198 0.2778 3765 X-RAY DIFFRACTION 100 2.4558-2.4858 0.3049 192 0.2718 3634 X-RAY DIFFRACTION 100 2.4858-2.5172 0.3207 192 0.2652 3667 X-RAY DIFFRACTION 100 2.5172-2.5503 0.2877 198 0.2507 3764 X-RAY DIFFRACTION 100 2.5503-2.5852 0.2438 192 0.2406 3643 X-RAY DIFFRACTION 100 2.5852-2.6221 0.2575 196 0.2289 3740 X-RAY DIFFRACTION 100 2.6221-2.6612 0.2571 194 0.2307 3675 X-RAY DIFFRACTION 100 2.6612-2.7027 0.3117 194 0.2305 3681 X-RAY DIFFRACTION 100 2.7027-2.747 0.2679 197 0.2172 3741 X-RAY DIFFRACTION 100 2.747-2.7943 0.2664 193 0.2201 3679 X-RAY DIFFRACTION 100 2.7943-2.845 0.2468 196 0.2129 3718 X-RAY DIFFRACTION 100 2.845-2.8996 0.2651 191 0.2171 3641 X-RAY DIFFRACTION 100 2.8996-2.9587 0.2395 199 0.2124 3770 X-RAY DIFFRACTION 100 2.9587-3.023 0.2344 194 0.211 3685 X-RAY DIFFRACTION 100 3.023-3.0932 0.2338 198 0.2042 3760 X-RAY DIFFRACTION 100 3.0932-3.1704 0.2417 193 0.2031 3673 X-RAY DIFFRACTION 100 3.1704-3.2559 0.2295 197 0.1936 3736 X-RAY DIFFRACTION 100 3.2559-3.3515 0.2078 195 0.1878 3721 X-RAY DIFFRACTION 100 3.3515-3.4594 0.2016 197 0.1852 3728 X-RAY DIFFRACTION 100 3.4594-3.5827 0.2168 196 0.184 3737 X-RAY DIFFRACTION 100 3.5827-3.7257 0.2108 196 0.1729 3713 X-RAY DIFFRACTION 100 3.7257-3.8947 0.1803 197 0.1561 3743 X-RAY DIFFRACTION 100 3.8947-4.0992 0.1861 197 0.1578 3740 X-RAY DIFFRACTION 100 4.0992-4.3547 0.1721 198 0.1448 3765 X-RAY DIFFRACTION 100 4.3547-4.6889 0.1694 199 0.1402 3788 X-RAY DIFFRACTION 100 4.6889-5.157 0.2002 199 0.1472 3784 X-RAY DIFFRACTION 100 5.157-5.8947 0.1942 201 0.1596 3803 X-RAY DIFFRACTION 100 5.8947-7.3945 0.214 201 0.1724 3834 X-RAY DIFFRACTION 100 7.3945-24.9619 0.179 209 0.1704 3964 X-RAY DIFFRACTION 100
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 12) 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 4.2114 0.7676 -0.0086 3.4788 -0.0123 4.0167 -0.1361 -0.2927 0.661 0.2535 0.1764 -0.1468 -0.8372 0.0305 -0.1435 0.4975 0.0425 -0.0412 0.2186 -0.0944 0.6001 19.2078 53.0763 18.2017 2 2.3887 0.5437 0.2171 1.715 0.2622 2.8562 -0.1981 0.1311 0.1014 0.0029 0.0737 0.3091 -0.0365 -0.4904 0.1411 0.2206 0.0442 -0.0213 0.3093 -0.0035 0.4473 14.7622 36.499 9.1071 3 3.1228 2.2018 1.4789 4.8023 0.3728 7.6652 -0.1642 0.3938 0.2493 -0.3248 0.2288 0.4738 -0.4938 0.5222 0.0325 0.2632 0.0013 -0.0595 0.6575 -0.0392 0.5421 -4.8688 29.7116 -6.3004 4 0.5639 -0.5242 -0.2306 -0.496 0.1729 7.8927 0.0548 -0.2128 -0.0517 -0.3237 0.0301 0.2293 -0.4949 -0.6932 -0.1361 1.2262 -0.1547 -0.2231 0.9997 0.0328 0.5266 -1.7003 30.9408 -50.6101 5 2.345 -1.0589 -0.8172 3.9145 0.6717 3.3142 -0.0945 -0.1402 -0.2477 0.1045 0.2099 -0.384 0.1628 0.4334 -0.11 0.2166 0.0083 -0.0477 0.4126 -0.0181 0.5587 47.5249 22.99 12.8424 6 1.4154 0.2865 0.8522 2.2935 -0.2162 2.2013 -0.2224 0.232 0.1395 -0.1198 0.1063 -0.1457 -0.2062 0.3962 0.1147 0.2234 -0.037 -0.0042 0.3572 0.0167 0.4549 33.2977 34.0122 4.8333 7 1.7688 0.6179 -0.6027 3.3703 0.603 2.2475 -0.1382 0.351 0.0408 -0.773 0.4324 0.2763 0.3783 -0.5334 -0.1082 0.7573 -0.3765 -0.1636 0.6668 0.1167 0.5422 31.7766 50.6228 -14.6735 8 1.543 0.1803 1.4876 0.0235 0.6238 4.7331 0.0588 -0.0346 0.0967 -0.1061 -0.0872 -0.0736 -0.9608 0.4232 0.0689 1.5706 -0.4025 -0.2718 0.8802 0.0344 0.5809 17.4987 38.8286 -55.1129 9 5.3411 -0.1681 0.236 2.6732 -0.3302 3.8192 -0.0053 -0.222 -0.2925 0.3155 0.2088 0.6885 0.5085 -0.917 0.0335 0.3577 -0.0654 0.1461 0.4714 0.1303 0.5358 8.9598 12.9535 20.8641 10 1.0088 -0.6237 0.1827 1.8983 -0.1235 5.7944 -0.0676 -0.0113 -0.0548 -0.1089 -0.0246 0.0175 0.2902 0.0752 0.0447 0.2472 -0.0223 0.0467 0.2524 0.0331 0.4452 22.1416 19.3618 8.3333 11 4.665 0.3064 2.21 2.3172 0.4334 4.4357 0.0862 0.3652 -0.0868 -0.4845 0.1085 -0.136 -0.5799 0.2705 -0.1818 0.5017 -0.0004 0.066 0.2594 0.0101 0.3763 31.1691 8.208 -13.7643 12 0.1178 -0.266 1.4859 0.4962 -0.4936 6.7644 0.0312 0.2914 -0.1445 -0.1792 0.0443 0.0416 0.2566 0.472 -0.116 1.2528 -0.0667 -0.2401 0.7925 0.0573 0.511 14.7112 18.2508 -54.3277
Refinement TLS group ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 (chain A and resseq 1:17) or (chain A and resseq 310:383)2 X-RAY DIFFRACTION 2 (chain A and resseq 18:35) or (chain A and resseq 259:309) or (chain A and resseq 384:410)3 X-RAY DIFFRACTION 3 (chain A and resseq 36:48) or (chain A and resseq 181:258) or (chain A and resseq 1410:1410)4 X-RAY DIFFRACTION 4 (chain A and resseq 49:180)5 X-RAY DIFFRACTION 5 (chain B and resseq 1:17) or (chain B and resseq 310:383) or (chain B and resseq 1412:1412) or (chain B and resseq 1413:1413)6 X-RAY DIFFRACTION 6 (chain B and resseq 18:35) or (chain B and resseq 259:309) or (chain B and resseq 384:410)7 X-RAY DIFFRACTION 7 (chain B and resseq 36:48) or (chain B and resseq