Software Name Version Classification NB SCALA3.3.20data scalingShow BUSTER-TNTBUSTER 2.10.0refinementShow PDB_EXTRACT3.11 data extractionShow Blu-IceEpicsdata collection MOSFLMdata reduction PHASERphasing BUSTER2.1 refinement
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : PDB ENTRY 3LYFResolution : 3.9→41.6 Å / Cor.coef. Fo :Fc : 0.5636 / Cor.coef. Fo :Fc free : 0.5121 / Occupancy max : 1 / Occupancy min : 1 / Cross valid method : THROUGHOUT / σ(F) : 0 / SU Rfree Blow DPI : 0.776 Rfactor Num. reflection % reflection Selection details Rfree 0.2484 1459 5.04 % SHELL Rwork 0.228 - - - obs 0.229 28958 99.17 % -
Displacement parameters Biso max : 300 Å2 / Biso mean : 55.482 Å2 / Biso min : 3 Å2 Baniso -1 Baniso -2 Baniso -3 1- 10.9485 Å2 7.4022 Å2 7.6542 Å2 2- - -19.1423 Å2 17.4195 Å2 3- - - 8.1938 Å2
Refine analyze Luzzati coordinate error obs : 0.881 ÅRefinement step Cycle : LAST / Resolution : 3.9→41.6 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 19084 1400 0 0 20484
Refine LS restraints Show large table (6 x 17) Hide large table Refine-ID Type Number Restraint function Weight Dev ideal X-RAY DIFFRACTION t_dihedral_angle_d9583 SINUSOIDAL2 X-RAY DIFFRACTION t_trig_c_planes478 HARMONIC2 X-RAY DIFFRACTION t_gen_planes2908 HARMONIC5 X-RAY DIFFRACTION t_it21001 HARMONIC20 X-RAY DIFFRACTION t_nbdX-RAY DIFFRACTION t_improper_torsionX-RAY DIFFRACTION t_pseud_angleX-RAY DIFFRACTION t_chiral_improper_torsion2768 SEMIHARMONIC5 X-RAY DIFFRACTION t_sum_occupanciesX-RAY DIFFRACTION t_utility_distanceX-RAY DIFFRACTION t_utility_angleX-RAY DIFFRACTION t_utility_torsionX-RAY DIFFRACTION t_ideal_dist_contact24161 SEMIHARMONIC4 X-RAY DIFFRACTION t_bond_d21001 HARMONIC2 0.008 X-RAY DIFFRACTION t_angle_deg28639 HARMONIC2 0.87 X-RAY DIFFRACTION t_omega_torsion1.65 X-RAY DIFFRACTION t_other_torsion3.19
LS refinement shell Resolution : 3.9→4.04 Å / Total num. of bins used : 15 Rfactor Num. reflection % reflection Rwork 0.2618 2804 - all 0.2618 - - obs - - 99.17 %
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 30) 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 -0.7882 0.6075 1.6313 2.2652 -1.4028 0.3834 -0.0298 -0.0476 0.1837 -0.04 -0.0209 -0.0224 -0.1576 -0.2349 0.0507 0.0617 -0.2864 -0.1079 -0.1757 -0.0421 -0.1247 31.3556 65.6398 10.9818 2 -1.836 3.1214 -0.7838 1.7056 3.1059 1.4989 0.0293 0.262 -0.1046 -0.2312 -0.0477 0.372 0.0537 0.057 0.0183 -0.5224 0.0029 0.1469 0.4967 -0.2025 -0.2718 0.047 56.0779 28.3966 3 4.4374 -0.1916 -0.7284 -2.1025 3.3632 1.7423 -0.0738 -0.1532 0.0888 0.4141 -0.1072 -0.1112 0.0802 0.3568 0.1809 0.1392 0.006 0.0098 -0.0005 -0.0654 -0.4729 15.4426 61.2589 45.1026 4 -0.3961 -0.3802 3.0961 1.6861 -1.144 -0.5478 0.0025 0.1725 0.1346 -0.1282 0.0008 -0.125 0.0382 0.1615 -0.0033 -0.1009 -0.1361 0.0246 -0.0161 -0.2859 -0.074 18.0122 -8.9528 16.0168 5 3.7227 -1.911 -2.6412 6.1362 -0.0609 1.0622 0.0545 -0.12 -0.0318 -0.0743 -0.1452 0.2513 0.0226 -0.4268 0.0907 -0.2338 -0.1358 0.0855 0.0362 -0.1333 -0.676 31.2683 19.9372 -2.8318 6 1.6273 -0.8591 0.4815 0.8852 -4.0113 3.2724 -0.0296 -0.2168 -0.3447 0.5258 0.0388 -0.4851 0.0194 -0.009 -0.0092 -0.5012 -0.0892 0.3008 -0.0162 0.2464 -0.5073 48.9552 11.5312 9.7662 7 1.2826 -2.2019 2.3141 -2.7151 7.205 3.4896 -0.0458 -0.0071 -0.4451 0.1789 -0.0358 -0.0359 -0.0453 0.0816 0.0817 -0.2299 0.1064 0.0202 -0.0231 0.0217 -0.2026 3.5548 44.1697 5.7364 8 10.4235 -1.9566 -0.1609 -6.1474 5.8738 3.1104 0.0068 -0.0832 0.0253 0.2023 0.0015 0.0273 -0.2374 -0.3146 -0.0082 -0.6699 0.1063 -0.2741 0.077 -0.1174 -0.5498 -13.2465 12.3193 -6.6831 9 2.5775 -0.1943 4.4104 6.1015 -0.3777 -0.4545 0.2072 0.3101 0.0144 -0.3298 -0.0232 -0.223 -0.3438 -0.1631 -0.184 -0.3689 -0.1253 0.0915 -0.9184 0.1328 0.0488 5.8238 13.9442 -20.2075 10 2.8937 -2.9358 1.1104 4.4947 0.1859 4.7237 0.0163 -0.1149 0.0137 0.0033 0.0526 0.0208 0.2666 -0.1102 -0.0688 0.0236 0.1071 0.0914 0.3191 -0.0574 0.1893 -4.865 59.6319 39.608 11 1.4791 0.3221 -0.146 1.1127 0.5358 0.4012 0.0264 0.012 0.0518 -0.0394 -0.0878 0.1334 -0.1036 -0.1049 0.0614 -0.1315 -0.0473 0.2807 -0.154 -0.066 0.1042 -12.4041 22.794 34.7962 12 -1.3588 1.8433 -2.7863 0.2602 2.4825 1.0986 0.017 -0.0657 -0.0422 0.0811 0.0291 0.0629 0.0693 -0.0195 -0.0461 0.2602 -0.116 0.2721 -0.1329 -0.2194 -0.3292 -2.9927 25.2571 55.9047 13 0.9534 -2.2014 1.9829 3.0881 -0.4042 0.9602 -0.0713 0.1493 -0.1388 0.022 -0.0446 -0.148 0.2114 -0.2182 0.116 -0.0573 0.1265 -0.1591 -0.0929 0.0969 -0.0062 -9.4506 1.6984 -12.5501 14 2.2898 -1.3177 -1.3076 -4.3637 4.4686 5.4167 -0.0061 -0.2671 0.1091 0.2805 0.0681 0.4869 -0.0927 -0.0315 -0.062 -0.4411 -0.2158 -0.2741 0.2646 -0.399 -0.421 -40.5647 11.5487 -29.5626 15 5.9991 0.173 -0.0592 -1.9208 2.456 1.2319 -0.0323 0.259 -0.0526 -0.3152 -0.1537 -0.2582 0.1274 0.2107 0.186 0.0048 -0.0576 -0.0921 0.1838 -0.1669 -0.6862 -25.4016 5.5209 -46.2278 16 4.9629 0.7378 -3.9811 -1.345 0.0042 4.4741 0.0308 -0.1792 0.1661 0.1297 -0.106 0.2619 -0.0589 -0.1377 0.0752 0.2511 0.0575 0.0265 0.4896 -0.0253 0.4349 -14.449 13.465 43.3021 17 0.8221 -0.9624 2.9972 0.0349 -1.5207 4.0343 -0.0267 0.1459 0.27 -0.26 0.0508 0.3725 -0.2081 -0.1139 -0.0241 -0.5198 -0.1391 0.0133 0.0458 -0.0712 -0.0833 9.0202 0.0112 16.4853 18 3.386 -1.9181 0.8627 -3.4289 3.2731 2.7374 -0.0166 -0.2956 -0.2171 0.2909 0.1354 0.2764 -0.165 0.1773 -0.1188 -0.2217 -0.0406 -0.1457 0.0535 -0.3114 -0.3427 19.8257 -4.307 36.6047 19 2.1188 1.8615 -0.7866 0.2411 2.3291 4.4469 0.0783 -0.0902 0.1508 -0.1051 -0.01 0.0899 0.1327 0.0155 -0.0683 -0.2298 0.0169 0.1777 0.0748 -0.1309 -0.3139 42.9118 22.7276 -7.0511 20 10.3319 0.6715 0.8362 -0.1791 1.1686 0.7865 -0.037 0.1562 -0.0815 -0.0452 0.0398 -0.0861 -0.0417 -0.27 -0.0029 -0.8257 0.0151 0.5144 -0.005 -0.158 -0.5809 27.3697 54.802 5.3854 21 5.6924 0.0805 3.5797 5.6372 0.4482 2.3359 0.0456 -0.4535 -0.162 0.193 0.3071 -0.1177 0.1453 0.1329 -0.3527 -0.5011 -0.0442 0.1578 -0.6239 0.0456 -0.0137 46.4485 53.132 18.8411 22 5.2833 2.7066 -2.5847 3.7608 -1.5871 4.0747 -0.0177 0.0914 0.0335 0.0042 0.0249 0.0569 -0.1396 -0.126 -0.0072 0.1399 -0.1676 -0.1989 0.246 -0.177 0.1704 -45.4873 7.7639 -40.6844 23 2.4751 0.0674 0.8643 1.1065 -2.4628 -0.5212 -0.0099 -0.0859 -0.053 0.0996 -0.0347 0.1742 0.0821 -0.0996 0.0446 -0.0472 -0.1162 -0.4199 -0.2526 -0.1302 0.08 -51.5392 44.8987 -36.7838 24 -1.7252 0.3736 4.7763 1.8997 -0.2589 -0.1746 0.0175 0.1131 0.1469 -0.1089 -0.0375 -0.059 -0.0989 -0.0263 0.02 0.4685 0.0231 -0.3117 -0.1951 -0.0432 -0.3808 -41.9874 41.7504 -57.5228 25 -0.3429 1.9162 -3.8574 3.1851 0.4816 0.1525 0.0518 -0.0838 -0.0127 0.0668 -0.0282 0.0468 -0.0617 -0.0087 -0.0235 -0.1561 -0.0645 -0.1462 -0.2156 -0.3257 -0.1308 -20.3426 76.1325 -17.5689 26 4.0937 3.1266 3.4775 2.9797 -0.511 1.3394 0.0641 0.1321 -0.1472 0.057 -0.3262 0.4759 0.0707 -0.5518 0.2621 -0.083 0.0927 0.1868 -0.2584 0.0582 -0.5275 -8.0493 47.225 1.5941 27 2.7724 -2.642 3.3602 0.2269 -3.157 6.8254 0.0584 0.2866 0.2346 -0.4129 -0.1257 -0.3363 -0.0546 0.0143 0.0673 -0.4449 -0.0599 0.0019 -0.0812 0.4022 -0.5336 9.7717 55.3065 -11.0854 28 3.908 0.3738 4.4559 1.1666 -2.1964 5.6397 0.0509 0.1646 -0.1598 -0.2126 -0.1131 0.2875 0.1359 -0.2193 0.0622 0.4658 0.0019 -0.1087 0.3668 -0.0315 0.4549 -53.164 54.3561 -45.0868 29 5.6747 -0.3615 -1.488 1.2778 -5.4465 -1.6575 -0.1798 -0.0482 -0.232 0.3396 0.2355 0.5267 0.3837 -0.1427 -0.0557 -0.6347 0.1192 -0.0193 0.0205 0.0637 -0.0562 -29.4504 67.311 -18.2041 30 1.9903 0.4064 0.9874 -1.5717 3.581 1.7414 -0.0364 0.2922 0.2188 -0.387 0.0223 0.3548 0.262 0.2866 0.0141 -0.2573 -0.0636 0.1557 0.1523 -0.1926 -0.2732 -18.0892 71.373 -38.1102
Refinement TLS group Show large table (6 x 30) Hide large table ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 {A|5 - 34} A5 - 34 2 X-RAY DIFFRACTION 2 {A|35 - 112} A35 - 112 3 X-RAY DIFFRACTION 3 {A|113 - 245} A113 - 245 4 X-RAY DIFFRACTION 4 {B|5 - 34} B5 - 34 5 X-RAY DIFFRACTION 5 {B|35 - 112} B35 - 112 6 X-RAY DIFFRACTION 6 {B|113 - 245} B113 - 245 7 X-RAY DIFFRACTION 7 {C|5 - 34} C5 - 34 8 X-RAY DIFFRACTION 8 {C|35 - 111} C35 - 111 9 X-RAY DIFFRACTION 9 {C|112 - 245} C112 - 245 10 X-RAY DIFFRACTION 10 {D|5 - 34} D5 - 34 11 X-RAY DIFFRACTION 11 {D|35 - 111} D35 - 111 12 X-RAY DIFFRACTION 12 {D|112 - 245} D112 - 245 13 X-RAY DIFFRACTION 13 {E|5 - 34} E5 - 34 14 X-RAY DIFFRACTION 14 {E|35 - 112} E35 - 112 15 X-RAY DIFFRACTION 15 {E|113 - 245} E113 - 245 16 X-RAY DIFFRACTION 16 {F|5 - 34} F5 - 34 17 X-RAY DIFFRACTION 17 {F|35 - 112} F35 - 112 18 X-RAY DIFFRACTION 18 {F|113 - 245} F113 - 245 19 X-RAY DIFFRACTION 19 {G|5 - 34} G5 - 34 20 X-RAY DIFFRACTION 20 {G|35 - 112} G35 - 112 21 X-RAY DIFFRACTION 21 {G|113 - 245} G113 - 245 22 X-RAY DIFFRACTION 22 {H|5 - 34} H5 - 34 23 X-RAY DIFFRACTION 23 {H|35 - 112} H35 - 112 24 X-RAY DIFFRACTION 24 {H|113 - 245} H113 - 245 25 X-RAY DIFFRACTION 25 {I|5 - 34} I5 - 34 26 X-RAY DIFFRACTION 26 {I|35 - 112} I35 - 112 27 X-RAY DIFFRACTION 27 {I|113 - 245} I113 - 245 28 X-RAY DIFFRACTION 28 {J|5 - 34} J5 - 34 29 X-RAY DIFFRACTION 29 {J|35 - 112} J35 - 112 30 X-RAY DIFFRACTION 30 {J|113 - 245} J113 - 245