Software | Name | Version | Classification |
---|
XDS | | data reductionXSCALE | | data scalingPHENIX | 1.18.2refinementPDB_EXTRACT | 3.25 | data extractionPHASER | | phasingCoot | | model building | | | | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: apo structure, pdb entry 6XNQ Resolution: 1.85→48.87 Å / SU ML: 0.1944 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.3754 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| Rfactor | Num. reflection | % reflection | Selection details |
---|
Rfree | 0.1901 | 2025 | 1.31 % | 0 |
---|
Rwork | 0.1567 | 152146 | - | - |
---|
obs | 0.1571 | 154171 | 99.16 % | - |
---|
|
---|
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
---|
Displacement parameters | Biso mean: 24 Å2 |
---|
Refinement step | Cycle: LAST / Resolution: 1.85→48.87 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 11971 | 0 | 260 | 1590 | 13821 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
---|
X-RAY DIFFRACTION | f_bond_d0.0087 | 12834 | X-RAY DIFFRACTION | f_angle_d0.9271 | 17541 | X-RAY DIFFRACTION | f_chiral_restr0.0608 | 2010 | X-RAY DIFFRACTION | f_plane_restr0.0075 | 2288 | X-RAY DIFFRACTION | f_dihedral_angle_d13.8536 | 4773 | | | | | |
|
---|
LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
---|
1.85-1.9 | 0.3025 | 151 | 0.2411 | 10748 | X-RAY DIFFRACTION | 98.7 | 1.9-1.95 | 0.2952 | 138 | 0.208 | 10769 | X-RAY DIFFRACTION | 98.51 | 1.95-2 | 0.2688 | 135 | 0.1838 | 10810 | X-RAY DIFFRACTION | 98.86 | 2-2.07 | 0.2171 | 136 | 0.1729 | 10780 | X-RAY DIFFRACTION | 98.78 | 2.07-2.14 | 0.1696 | 158 | 0.1682 | 10809 | X-RAY DIFFRACTION | 99.2 | 2.14-2.23 | 0.1851 | 158 | 0.1594 | 10850 | X-RAY DIFFRACTION | 99.11 | 2.23-2.33 | 0.1663 | 143 | 0.1515 | 10802 | X-RAY DIFFRACTION | 99.29 | 2.33-2.45 | 0.2044 | 151 | 0.1518 | 10912 | X-RAY DIFFRACTION | 99.4 | 2.45-2.61 | 0.1801 | 161 | 0.1533 | 10886 | X-RAY DIFFRACTION | 99.54 | 2.61-2.81 | 0.1878 | 134 | 0.1558 | 10878 | X-RAY DIFFRACTION | 99.62 | 2.81-3.09 | 0.1854 | 135 | 0.1571 | 10990 | X-RAY DIFFRACTION | 99.75 | 3.09-3.54 | 0.1878 | 156 | 0.1504 | 10937 | X-RAY DIFFRACTION | 99.7 | 3.54-4.46 | 0.1679 | 143 | 0.1348 | 10977 | X-RAY DIFFRACTION | 99.42 | 4.46-48.87 | 0.1743 | 126 | 0.1509 | 10998 | X-RAY DIFFRACTION | 98.45 |
|
---|
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION 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 | 3.48361170993 | 1.79419722917 | -0.879838672403 | 3.58275681251 | 0.692402427715 | 2.41969508221 | -0.0679108763948 | -0.0271081498048 | 0.372000722788 | -0.0744796353748 | 0.0432079968263 | -0.142432081932 | -0.562170278444 | 0.0141396342645 | -0.0077729640049 | 0.250488046389 | 0.0557940236289 | -0.0294768323167 | 0.129849358787 | 0.0126762211135 | 0.239920669116 | 5.49494641512 | 37.1890685608 | 48.8945930505 | 2 | 1.52323457406 | -1.04591923882 | -0.0511218917574 | 2.16917185884 | 0.14667362789 | 0.514404232461 | -0.0934509571638 | -0.108900035245 | 0.115393931558 | 0.14709867145 | 0.0999174093899 | 0.115640120589 | -0.076645081951 | -0.0521690381608 | -0.00170896275954 | 0.133577986452 | 0.0546679816131 | 0.0165534706406 | 0.148161362596 | 0.0132001312225 | 0.135896154507 | 5.50961448888 | 21.0714973713 | 50.563241675 | 3 | 0.533921410857 | -0.0696470639079 | -0.477342930273 | 2.46987125694 | 1.20763064488 | 3.02886487751 | 0.0221014518479 | -0.0773541855947 | 0.1351467487 | -0.122772829557 | 0.116731118424 | -0.339751525542 | -0.398709969454 | 0.267934581914 | -0.0865486775714 | 0.186652876271 | 0.0279469695343 | -0.0125837648467 | 0.158197381496 | 0.0106105001392 | 0.258776309248 | 13.9558380045 | 33.6125277467 | 47.7879764025 | 4 | 0.91209076923 | -1.10439876337 | 0.124547022645 | 1.16713989733 | -0.0846677622182 | -0.0107395322318 | -0.252760786921 | -0.347043940527 | 0.23390463045 | 0.0419991338415 | 0.213546763326 | -0.10467172741 | -0.330244084762 | -0.0441675661566 | 0.0103173569759 | 0.30366593614 | 0.0980866143934 | 0.00160806803992 | 0.20038374874 | -0.05116948353 | 0.173618087245 | 16.0451051571 | 24.1976500612 | 62.3573158899 | 5 | 1.61553105673 | 0.374790694065 | -0.120228566838 | 0.906118463557 | 0.102923441587 | 0.967099052904 | 0.00781565483343 | -0.13125829418 | 0.1077295464 | 0.210928312648 | 0.0402406063059 | 0.148236780635 | -0.108336186289 | -0.0800792265962 | -0.0497225651053 | 0.175893845273 | 0.0750192253693 | 0.0326943570366 | 0.150277957785 | 0.0221830143496 | 0.119655814535 | 14.1980476921 | 7.55982492952 | 63.2319866412 | 6 | 0.0234009246045 | -0.0741498613328 | -0.0922771577843 | 0.622987669751 | 0.18119682676 | 0.400589054936 | -0.0235652807933 | -0.0157991898494 | 0.00767999155182 | 0.0350420599799 | 0.0354777881522 | 0.0647254064997 | 0.00164960188901 | -0.0520587595962 | -0.0104273023293 | 0.114512794541 | 0.0332045836644 | 0.00771324735206 | 0.149952015596 | 0.0201105466743 | 0.137446489798 | 13.8385908823 | 1.21536569945 | 44.8654702947 | 7 | 0.771540554672 | 0.768258457302 | 0.777464138509 | 2.08905062034 | 1.15359787023 | 2.92462806682 | 0.106731654965 | -0.0986481280145 | -0.108665394436 | 0.213350196079 | -0.00492360008693 | 0.0687774335777 | 0.29648646239 | -0.340506929135 | -0.0469490684314 | 0.141194003253 | 0.0202548090135 | 0.0288018109834 | 0.166939005727 | 0.0406600040073 | 0.153000756156 | 9.90174805364 | -10.4406947099 | 57.4556803891 | 8 | 2.1917881133 | -0.584647292826 | -1.50554815717 | 0.281462180423 | 0.519565073018 | 4.08543120228 | -0.00226152583191 | -0.179065706655 | -0.320929464147 | 0.0408001215712 | -0.037194811092 | -0.24207230744 | 0.11704039115 | 0.096372771964 | 0.0397464203834 | 0.306590780449 | 0.0793597144421 | -0.0114838846054 | 0.218222490934 | -0.00104096664256 | 0.238492562597 | 37.8563026261 | -22.3251657505 | 34.9939030403 | 9 | 3.50050576798 | 1.64614318458 | 1.11396630009 | 3.90019652662 | -0.265470731297 | 2.3162331001 | -0.0166137693401 | 0.039649325717 | -0.40954667396 | -0.120388044308 | 0.05690401122 | -0.0281037365108 | 0.471791804021 | 0.0412644980553 | -0.0574753129801 | 0.221232297161 | 0.0649572615679 | 0.0152173110319 | 0.122467383154 | 0.0324350654566 | 0.196865258706 | 41.5380891943 | -37.7888146213 | 51.9891423011 | 10 | 1.25861020757 | -0.705581481342 | 0.660384652079 | 6.40168789947 | -0.517315350093 | 1.28582256385 | -0.128872285121 | -0.279163992409 | -0.0763879979434 | 0.601271491039 | 0.0536952055172 | -0.139246534706 | -0.0395329851987 | -0.123349635356 | 0.0665514296356 | 0.214632720015 | 0.0722058737414 | -0.0119298582983 | 0.202339308555 | 0.0422902896402 | 0.16254846463 | 45.8495295121 | -30.1192346958 | 61.6055152278 | 11 | 1.63505524453 | 0.0631760084034 | 0.116338877949 | 2.5101208246 | 0.0714047925521 | 1.4680194951 | -0.0578983554645 | 0.0334827512784 | 0.0703629054867 | 0.0911855629158 | 0.0710734294201 | -0.0403446551807 | -0.0277053734149 | 0.0572336468839 | -0.000287022047176 | 0.100144912459 | 0.0272759807745 | -0.00030468670113 | 0.0819878941686 | 0.00719437344538 | 0.0429678341449 | 36.8271413216 | -9.12438807383 | 52.8883366958 | 12 | 0.395787870533 | 0.0393373806731 | 0.398569795363 | 2.47632625372 | -0.357461109521 | 1.48910547026 | -0.0351294501416 | 0.0435978210465 | -0.128769887497 | -0.187898276979 | 0.0127904686128 | 0.0223563341845 | 0.222079438339 | 0.0920848300961 | -0.00842664158933 | 0.15044668275 | 0.0520091845504 | 0.00847925810105 | 0.115957435682 | 0.0182481778536 | 0.14288701341 | 39.4566429566 | -27.2630408061 | 45.7862161245 | 13 | 0.136122785799 | -0.476191117086 | -0.153490002018 | 2.13078797282 | -0.151154865821 | 0.457830097347 | -0.0763927513472 | -0.0554347482145 | 0.12670199393 | 0.0838039405508 | 0.156747343615 | 0.0908251520822 | 0.188516917899 | -0.140123063914 | -0.0396646010028 | 0.34288315732 | -0.0212228667838 | 0.0231400946451 | 0.277640485832 | 0.07143152197 | 0.288195200928 | 29.4074453971 | -40.3092843866 | 61.0855256929 | 14 | 1.01177437288 | -0.144230445176 | 0.58272484952 | 0.374574525315 | 0.178924954766 | 1.52516307189 | 0.0677793812685 | -0.164584878729 | -0.106249637387 | 0.138653898229 | 0.00855789153295 | 0.0950463481977 | 0.0317443373844 | -0.205026068353 | -0.0773866341936 | 0.186649286832 | 0.0187367375238 | 0.0180120411044 | 0.151026819316 | 0.0524251906 | 0.119653876801 | 24.5433041054 | -15.6381881777 | 66.264992499 | 15 | 1.83605268444 | 0.684997475205 | 0.33964296847 | 1.04556037295 | 0.0696866215996 | 0.907260709203 | 0.011621743732 | -0.0260412767854 | -0.0994835539137 | 0.215140063478 | 0.0410231418764 | -0.0324382576467 | 0.0122974146241 | 0.0844717305205 | -0.0649506811593 | 0.151752822657 | 0.0507671867124 | -0.0112765676396 | 0.108748909856 | 0.0108226404489 | 0.0950428771922 | 33.9876189254 | -7.17874536363 | 62.0804106207 | 16 | 0.134111786779 | -0.00284389834588 | -0.170313364124 | 0.551726964399 | -0.0798905343739 | 0.382622480539 | -0.0134140203266 | -0.0279944290187 | 0.0133724924967 | 0.0389848377441 | 0.0197159754575 | 0.0198541343271 | -0.0554490467995 | -0.0163704364893 | -0.0113192237281 | 0.11716616732 | 0.0261753627366 | -0.0132387977383 | 0.128093409502 | 0.008169790383 | 0.0952416230113 | 34.5283853969 | -1.76507429312 | 46.9826045046 | 17 | 1.23344077261 | 0.94554473701 | -0.844528633136 | 1.58005103622 | -0.570063165558 | 1.68712349975 | 0.108625677215 | -0.195128676041 | 0.173173775482 | 0.179656449132 | -0.00674897143079 | 0.0828802793593 | -0.338109678064 | 0.203600885763 | -0.0980890837023 | 0.16475646378 | 0.0271925942705 | -0.0142647550848 | 0.119336435903 | -0.00917030131276 | 0.105316327595 | 35.7982922712 | 9.54398997015 | 60.3816299861 | 18 | 5.81410668646 | 2.59001273178 | 0.111906688146 | 2.98828700022 | -0.0294975707277 | 1.24877287504 | 0.234118060205 | -0.327051748948 | 0.251849407281 | 0.259691842879 | -0.213286369261 | 0.289867645967 | -0.152494155871 | -0.290817397394 | -0.00406377637708 | 0.311572620588 | 0.105193523232 | 0.0411983228415 | 0.240255566304 | 0.0605727262426 | 0.220302671759 | 13.4716284922 | 22.2642055493 | 33.4810300957 | 19 | 3.01387823894 | -0.737255179671 | -0.626981677486 | 3.54378068927 | -0.19682103154 | 1.51203879729 | -0.0152309611932 | 0.123508480558 | 0.386202737124 | 0.0249430789781 | -0.023586162807 | -0.2845070037 | -0.458626299535 | 0.10513008653 | -0.0274480825686 | 0.289301749332 | -0.0782880883712 | -0.0301937921757 | 0.148983594892 | 0.0382975408822 | 0.192594104993 | 47.1472160794 | 34.1727662651 | 21.0937464467 | 20 | 0.75039147336 | 0.182755494484 | -0.140010183776 | 2.20563845519 | 0.0489665814942 | 1.34390805398 | -0.0380845306517 | -0.0382550644382 | 0.122369641502 | 0.0750723134144 | 0.0533626680917 | -0.0648397253221 | -0.260587778605 | 0.115384742682 | -0.0235135071989 | 0.143778493785 | -0.018410759991 | -0.0152637841384 | 0.102293995364 | 0.0108357448172 | 0.0891103300352 | 40.7698104981 | 20.8750563604 | 27.7740184 | 21 | 0.000364635243425 | 0.0532503272833 | 0.0139429964001 | 2.0695491132 | -0.0639343204979 | 0.450159646788 | -0.0271574849289 | 0.0666381834965 | 0.16866946676 | -0.0950674547434 | 0.0897951121723 | 0.136819230027 | -0.387792790745 | -0.105800341899 | -0.0376435060969 | 0.35525508154 | 0.018836753505 | 0.0170028609368 | 0.198851497133 | 0.0507158195074 | 0.195813410939 | 35.0865582306 | 32.1891138446 | 13.4095449344 | 22 | 1.16995625505 | -0.166727492113 | -0.215593327834 | 0.749275773264 | -0.0717145390077 | 1.17497658962 | 0.0137916507726 | 0.141539248108 | 0.0931086682369 | -0.193926942965 | 0.0201620833456 | -0.00488127278138 | -0.0872505140122 | -0.0416876521794 | -0.0242565589629 | 0.177376940967 | -0.0350741802404 | 0.00545733897063 | 0.133005041318 | 0.0225136654439 | 0.109360212274 | 35.554570397 | 8.8223126599 | 9.84648165337 | 23 | 0.0489972745066 | 0.00301217548562 | -0.0288194827147 | 0.572731883252 | -0.264646592013 | 0.755183769151 | -0.0180783814592 | 0.0196014583245 | -0.0113328402014 | -0.0281086564918 | 0.0194486608817 | -0.00550573177525 | 0.00754611422616 | -0.000777695324053 | -0.00770372773451 | 0.0974201711774 | -0.00388508380576 | -0.00205513885645 | 0.118376773297 | 0.00377661861035 | 0.0930204327958 | 36.4500542143 | 1.41048254296 | 28.058272951 | 24 | 0.960350802163 | -0.581573792879 | 0.675915494615 | 1.764265191 | -1.1614223065 | 2.60489858476 | 0.0673588072941 | 0.119768453015 | -0.0819343349283 | -0.224633482438 | -0.0191433002273 | -0.0356549974665 | 0.341708956499 | 0.22869399444 | -0.0235335327971 | 0.163173454344 | -0.0100930576628 | 0.0109041184213 | 0.142044023019 | -0.0184085172371 | 0.104665159423 | 40.4784283609 | -9.90115900705 | 15.3098827506 | 25 | 4.27294511359 | -0.729889749574 | -0.778182798545 | 3.18637907291 | -0.324230489567 | 3.17379432708 | 0.19432649022 | 0.42674753676 | -0.0663266720982 | -0.12899391386 | -0.16960340509 | 0.258780304241 | 0.212405515557 | -0.358421324233 | -0.0220901921411 | 0.298899070681 | -0.080134662347 | -0.0230910670992 | 0.268369266144 | 0.0416857122253 | 0.192662619903 | 13.1259957766 | -22.6159312039 | 37.1836039114 | 26 | 2.71939352768 | 0.135521915541 | 0.732666707011 | 4.56852607753 | 0.399702367421 | 2.66343226681 | -0.185195347766 | 0.268184297927 | -0.4689569277 | -0.250305201457 | 0.140410933704 | -0.17588520385 | 0.346156150638 | -0.0243517609518 | 0.0219692052804 | 0.211158385555 | -0.0976345195023 | 0.0379601326608 | 0.206559992077 | -0.0455982710885 | 0.254819300631 | 7.83569798478 | -34.9282416685 | 16.4458248035 | 27 | 0.943609167104 | 1.19282432288 | 0.00680199486294 | 2.52861859654 | 0.105011717034 | 0.926722505502 | -0.059451784209 | 0.0459358785771 | -0.14056310617 | 0.0295877756386 | 0.0825775303959 | 0.0261278110533 | 0.130129244278 | -0.159633117529 | -0.00743995248866 | 0.123458460354 | -0.0453817401418 | -0.00772262690985 | 0.16803812505 | 0.00520013235734 | 0.145795794091 | 10.5425478782 | -21.7828928344 | 23.5006180767 | 28 | 1.32521335271 | 2.19447017629 | -0.910204271933 | 4.41489668494 | -0.310031623055 | 1.86363192225 | -0.469068496293 | 0.0605148925244 | -0.172385623196 | -0.292891244194 | 0.346539026225 | -0.517340430465 | 0.244614397627 | -0.0754406431678 | 0.115419687107 | 0.334957686189 | -0.00446577547419 | 0.0999696909841 | 0.273677268516 | -0.0933188858134 | 0.411349781706 | 20.8748441288 | -39.7483954605 | 10.5780510975 | 29 | 1.60962288496 | -0.403699603126 | 0.131277170533 | 1.00701225029 | -0.0650125336169 | 0.847486002276 | -0.0279463609226 | 0.169418393231 | -0.100854608742 | -0.18425446745 | 0.062906206116 | 0.0940598266016 | 0.0872958879621 | -0.104139874793 | -0.045852803645 | 0.182120134291 | -0.0562084939097 | -0.0294101748175 | 0.167467208816 | -0.000558522952936 | 0.0997080821732 | 20.1476675428 | -9.98546852527 | 8.72757880492 | 30 | 0.00349722248177 | -0.00781528676697 | -0.10873241345 | 0.281779557296 | 0.108496596531 | 0.363372291162 | -0.0140918179507 | 0.0620979427343 | 0.0124750200081 | -0.0521089564459 | 0.0491311232774 | 0.0770266293678 | -0.0214432059721 | -0.0884855651325 | -0.0339442185313 | 0.109126341135 | -0.00583628288013 | -0.0252087479742 | 0.160620733545 | 0.0228625689133 | 0.125611332261 | 15.7519872261 | -1.57203807213 | 25.9185556858 | 31 | 0.323629089035 | 0.265998987014 | 0.268041093002 | 0.613558153122 | 0.236024363673 | 1.23156169673 | 0.00600309371642 | -0.0043556242112 | 0.0888938779384 | 0.00590574545337 | 0.0633287241044 | -0.00418983665097 | -0.21567532657 | 0.0209277986697 | -0.0317661658641 | 0.206197052389 | 0.00933075792197 | 0.0166553683703 | 0.160813757215 | 0.0147967909294 | 0.169647036667 | 25.3624311094 | 15.5437848309 | 26.1064283054 |
|
---|
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION ID | Refine TLS-ID | Selection details | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
---|
1 | 1 | chain 'A' and (resid 3 through 40 )AA3 - 40 | 1 - 38 | 2 | 2 | chain 'A' and (resid 41 through 125 )AA41 - 125 | 39 - 123 | 3 | 3 | chain 'A' and (resid 126 through 165 )AA126 - 165 | 124 - 163 | 4 | 4 | chain 'A' and (resid 166 through 194 )AA166 - 194 | 164 - 192 | 5 | 5 | chain 'A' and (resid 195 through 277 )AA195 - 277 | 193 - 275 | 6 | 6 | chain 'A' and (resid 278 through 334 )AA278 - 334 | 276 - 332 | 7 | 7 | chain 'A' and (resid 335 through 378 )AA335 - 378 | 333 - 363 | 8 | 8 | chain 'A' and (resid 379 through 405 )AA379 - 405 | 364 - 390 | 9 | 9 | chain 'B' and (resid 4 through 40 )BJ4 - 40 | 1 - 37 | 10 | 10 | chain 'B' and (resid 41 through 67 )BJ41 - 67 | 38 - 64 | 11 | 11 | chain 'B' and (resid 68 through 92 )BJ68 - 92 | 65 - 89 | 12 | 12 | chain ' | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|