Software | Name | Version | Classification |
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PHENIX | 1.20.1_4487refinementautoPROC | 20230614 | data processingXDS | | data reductionSTARANISO | | data scalingAimless | | data scalingPHASER | | phasing | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→61.6 Å / SU ML: 0.2094 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3558 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2279 | 6816 | 4.97 % |
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Rwork | 0.1851 | 130367 | - |
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obs | 0.1873 | 137183 | 67.93 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Displacement parameters | Biso mean: 32.57 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.74→61.6 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 14681 | 0 | 126 | 1385 | 16192 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.0047 | 16343 | X-RAY DIFFRACTION | f_angle_d0.723 | 22130 | X-RAY DIFFRACTION | f_chiral_restr0.0491 | 2371 | X-RAY DIFFRACTION | f_plane_restr0.0064 | 2881 | X-RAY DIFFRACTION | f_dihedral_angle_d13.2994 | 6176 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.74-1.76 | 0.2912 | 11 | 0.3325 | 252 | X-RAY DIFFRACTION | 3.96 | 1.76-1.78 | 0.4398 | 23 | 0.3066 | 329 | X-RAY DIFFRACTION | 5.35 | 1.78-1.8 | 0.4166 | 23 | 0.2977 | 463 | X-RAY DIFFRACTION | 7.27 | 1.8-1.82 | 0.3638 | 35 | 0.271 | 561 | X-RAY DIFFRACTION | 9.05 | 1.82-1.85 | 0.2275 | 37 | 0.2479 | 690 | X-RAY DIFFRACTION | 10.83 | 1.85-1.87 | 0.3188 | 42 | 0.2425 | 965 | X-RAY DIFFRACTION | 15.12 | 1.87-1.9 | 0.339 | 75 | 0.2426 | 1343 | X-RAY DIFFRACTION | 21.33 | 1.9-1.93 | 0.3342 | 105 | 0.2444 | 2049 | X-RAY DIFFRACTION | 32.21 | 1.93-1.96 | 0.3001 | 128 | 0.249 | 2530 | X-RAY DIFFRACTION | 40.02 | 1.96-1.99 | 0.2713 | 164 | 0.24 | 2852 | X-RAY DIFFRACTION | 45.34 | 1.99-2.02 | 0.2852 | 174 | 0.2239 | 3300 | X-RAY DIFFRACTION | 51.57 | 2.02-2.06 | 0.278 | 211 | 0.2221 | 3691 | X-RAY DIFFRACTION | 58.88 | 2.06-2.1 | 0.2367 | 215 | 0.2237 | 4365 | X-RAY DIFFRACTION | 68 | 2.1-2.14 | 0.2857 | 271 | 0.2245 | 4933 | X-RAY DIFFRACTION | 78.49 | 2.14-2.19 | 0.2436 | 266 | 0.2252 | 5668 | X-RAY DIFFRACTION | 88.16 | 2.19-2.24 | 0.2827 | 311 | 0.2204 | 6123 | X-RAY DIFFRACTION | 95.83 | 2.24-2.3 | 0.2653 | 326 | 0.2227 | 6264 | X-RAY DIFFRACTION | 98.77 | 2.3-2.36 | 0.2541 | 372 | 0.2181 | 6316 | X-RAY DIFFRACTION | 99.67 | 2.36-2.43 | 0.2738 | 349 | 0.2135 | 6359 | X-RAY DIFFRACTION | 99.64 | 2.43-2.51 | 0.2527 | 331 | 0.206 | 6361 | X-RAY DIFFRACTION | 100 | 2.51-2.6 | 0.2682 | 313 | 0.2031 | 6412 | X-RAY DIFFRACTION | 100 | 2.6-2.7 | 0.2417 | 326 | 0.196 | 6423 | X-RAY DIFFRACTION | 99.99 | 2.7-2.82 | 0.2604 | 326 | 0.2005 | 6434 | X-RAY DIFFRACTION | 100 | 2.82-2.97 | 0.2315 | 321 | 0.1968 | 6451 | X-RAY DIFFRACTION | 99.94 | 2.97-3.16 | 0.2342 | 326 | 0.1958 | 6421 | X-RAY DIFFRACTION | 99.99 | 3.16-3.4 | 0.2146 | 345 | 0.1723 | 6445 | X-RAY DIFFRACTION | 99.82 | 3.4-3.74 | 0.2112 | 361 | 0.1576 | 6442 | X-RAY DIFFRACTION | 99.88 | 3.74-4.28 | 0.1774 | 332 | 0.1417 | 6507 | X-RAY DIFFRACTION | 99.99 | 4.28-5.4 | 0.1769 | 352 | 0.1378 | 6586 | X-RAY DIFFRACTION | 100 | 5.4-61.6 | 0.1952 | 345 | 0.1754 | 6832 | X-RAY DIFFRACTION | 99.5 |
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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) |
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1 | 2.93816956244 | -0.555251242675 | -0.0444549948542 | 0.731088588225 | -0.452563689243 | 0.334750353967 | -0.129908597644 | -0.731703817664 | 0.289070928134 | 0.302466668811 | 0.0117826583344 | 0.502704147273 | -0.0370627354113 | -0.160641802629 | -0.605429793168 | 0.102049961384 | 0.0248895968894 | 0.158205697576 | 0.343354449769 | -0.113233958273 | 0.682466213067 | -8.3583690528 | 23.8879678056 | 21.1436916909 | 2 | 1.29818702255 | 0.482531563619 | 0.0858119088165 | 0.705924058951 | 0.465933334445 | 1.23234491411 | -0.155750006188 | -0.492435447075 | 0.354962066205 | 0.358459253594 | -0.252310440952 | 1.07278334031 | -0.0996621161212 | -0.484785873807 | -0.230726453271 | 0.0723714393375 | -0.0332104031779 | 0.232280064449 | 0.244096055483 | -0.0900584114664 | 0.684556600079 | -0.379979946317 | 25.6894443494 | 23.2307992784 | 3 | 0.740767277121 | 0.198590077338 | 0.864667812983 | 0.0531300725807 | 0.233367066495 | 1.01289161503 | -0.021221518739 | -0.853531897433 | 0.606520071935 | 0.711336993194 | -0.154778392711 | 0.686740582092 | -0.0497987515958 | -0.612222659385 | -0.0875111761553 | 0.601292693748 | -0.0468283573255 | 0.413058471662 | 0.777508561463 | -0.298852705391 | 1.22929376339 | -2.85058991528 | 30.4991423258 | 33.9889349167 | 4 | 1.03507188274 | 0.122161665462 | -0.126492566233 | 0.850739653568 | -0.460547841884 | 0.422687328368 | 0.0862183317205 | -0.552387986301 | 0.149719015852 | 0.43708926326 | -0.326325199734 | -0.179937597466 | -0.0852308282352 | 0.112984853446 | -0.0955688608994 | 0.238853641633 | -0.0987832593658 | -0.0618401895642 | 0.28879802357 | 0.0891655263179 | 0.0816715993322 | 52.3022506117 | 27.1640738204 | 17.4943776628 | 5 | 1.96987410944 | -0.197899044676 | 0.364465735614 | 0.994368837419 | -0.221453164009 | 0.859417617398 | 0.0227193783425 | 0.124946056715 | -0.257272712215 | -0.260265264194 | -0.0811449488491 | -0.465074306269 | -0.039374630084 | 0.0545949468962 | 0.0336720781218 | 0.139159627151 | 0.0227284782961 | 0.109621307756 | 0.114206081223 | 0.021277997793 | 0.204990570018 | 54.0964552186 | 9.87277047987 | -6.57059781703 | 6 | 0.763648744256 | 0.299422494084 | 0.0716987418906 | 1.08305838454 | 0.0722369842292 | 0.328409635646 | 0.0955747280061 | 0.15617654155 | -0.0698618265358 | -0.0818694364366 | -0.0629325277203 | -0.795522260525 | 0.0348888671495 | 0.0970679818909 | 0.0109160877061 | 0.108934837663 | 0.0329025938422 | 0.235367614733 | 0.187638171968 | 0.127522239615 | 0.147463679353 | 58.2474162487 | 21.2181638036 | -7.30752040307 | 7 | 0.325467770522 | 0.441113884975 | -0.0632559059808 | 1.52794549265 | -0.192085997921 | 1.12796851768 | 0.059045738676 | -0.245606246319 | -0.0535210455084 | 0.129677566225 | -0.309834024096 | -1.0522197607 | 0.150254052097 | 0.539522178102 | -0.00863593427851 | 0.160439230853 | -0.0327565281475 | -0.0611186745723 | 0.36049226217 | 0.17201497849 | 0.496529087789 | 70.2808033938 | 25.3873069901 | 12.5807446478 | 8 | 0.142839149923 | 0.121658219143 | -0.277928500765 | 0.995123722696 | -0.720394527686 | 0.809268221294 | -0.0794342290172 | -0.540084900566 | -0.54707965301 | 0.472775346478 | -0.119263686382 | -0.647695466734 | -0.0778958914303 | 0.467373349002 | 0.221401886218 | 0.30399142383 | -0.0336985432379 | -0.108970621574 | 0.530812608618 | 0.221284316406 | 0.830502273381 | 69.7407002868 | 22.1418709629 | 20.0192456907 | 9 | 1.34820653142 | 0.134408336488 | -0.0993548879654 | 1.61757269166 | -0.211520578885 | 0.617917972158 | 0.0314154816646 | 0.113018239245 | -0.03395606168 | -0.0853659405555 | -0.0427716477332 | 0.0721800683114 | 0.0906102229479 | 0.0174198265416 | -0.00288042655909 | 0.132358682957 | -0.0138973207695 | -0.00622681062371 | 0.0713061618843 | 0.00521758345081 | 0.0179587096759 | 31.3948702323 | 10.5750951704 | 9.48222637408 | 10 | 1.28769107794 | -1.33021561155 | 0.15465966324 | 1.37790277504 | -0.168893742423 | 1.09833993635 | 0.00201835397581 | -0.0217021452911 | -0.309733344023 | 0.158421113355 | -0.111913349684 | -0.487225493602 | 0.00467176077863 | 0.212023613081 | 0.0334224194849 | 0.125911236287 | 0.0206561736832 | -0.0360386595863 | 0.134317565135 | 0.0923009768687 | 0.299835287634 | 47.3395927571 | -10.6950300013 | 11.2546441129 | 11 | 0.785594096877 | 0.10823635834 | -0.136267950677 | 1.50397271332 | -0.186756644104 | 0.557723482422 | 0.0984913860972 | -0.144113683235 | -0.293209189653 | 0.321036359762 | -0.196849809466 | 0.0740277334436 | 0.0693797024493 | 0.060680217466 | -0.0414312858451 | 0.136607860727 | -0.0074686152202 | -0.0172815422852 | 0.0762879136883 | 0.0883127165587 | 0.131907089105 | 34.4655630046 | -4.98602926355 | 17.5376397279 | 12 | 1.68032800351 | -0.0487523810811 | -0.300847010894 | 1.53705732462 | -0.365104072957 | 2.24027393599 | -0.231069566565 | 0.56017800373 | -0.881709982349 | -0.946178505635 | -0.0881716933877 | 0.132428721203 | 0.838312547584 | 0.198974745956 | -0.127553953134 | 0.425803832501 | -0.0797002079267 | 0.0838441821434 | 0.179757523424 | -0.144790866158 | 0.414344985042 | 26.6469722334 | -5.88370793575 | -2.89795495927 | 13 | 1.14618732616 | 0.0197241115159 | 0.232475665366 | 1.87190062208 | -0.0885799571219 | 0.924399158243 | -0.0419800157804 | 0.291320652291 | 0.324991695863 | -0.161369439496 | 0.0315088162181 | -0.0688319956728 | -0.116885967271 | 0.0465174677988 | -0.028654883409 | 0.128084753858 | -0.021894441835 | 0.0174496317025 | 0.171632677117 | 0.0556781382961 | 0.127786716871 | 36.1847439852 | 44.1381179185 | 8.44624568049 | 14 | 0.913476683803 | -0.238301152392 | -0.12361193382 | 1.41310991543 | 0.157298191647 | 0.61342051046 | -0.124271663089 | -0.474685307081 | 0.401276185454 | 0.26333716866 | -0.00383631087747 | -0.047751225908 | -0.126913648241 | -0.0102839940666 | -0.0024787473274 | 0.316407291038 | 0.0277268351571 | -0.0515819404438 | 0.263695797199 | -0.207480635396 | 0.257791684913 | 26.5609458534 | 55.5609329967 | 31.3055340659 | 15 | 1.39027268365 | 0.348281141306 | 0.120014418285 | 0.944034884316 | 0.279226626256 | 0.42231496934 | -0.0163011011293 | -0.0226655865246 | 0.863297163335 | 0.0746388713951 | 0.00991655948442 | 0.0849585843974 | -0.255582514473 | -0.0418279787468 | -0.0444191679935 | 0.238702284973 | -0.0291630341014 | -0.000164100765876 | 0.128790336605 | -0.00398345476952 | 0.461106129763 | 36.4734831865 | 58.4437308481 | 12.1206709809 | 16 | 1.17180470757 | -0.226073506186 | -0.0167488448562 | 0.319097968422 | -0.11008287244 | 1.04493294053 | 0.0148950261932 | -0.552231430332 | -0.159104851312 | 0.558964162748 | -0.107231592961 | 0.459162575667 | 0.0882133040995 | -0.375599855229 | 0.0465198970922 | 0.347275712953 | -0.0608177875376 | 0.251067231066 | 0.348537382449 | 0.0176280650094 | 0.22538669599 | 12.3333049554 | 19.5726386961 | 24.4628267258 | 17 | 1.08237798657 | -0.060886603408 | -0.540411843036 | 1.88305596561 | -0.448002532229 | 0.671914678051 | 0.0264052623877 | 0.10279956766 | -0.0958652607595 | -0.0481063477405 | -0.0497620822227 | 0.0655282725418 | -0.0256524008405 | -0.00199115018758 | 0.0274036773173 | 0.0713193431619 | 0.00726895851145 | 0.0108856919924 | 0.0856072135557 | 0.0224999569538 | 0.055986565617 | 19.0971070705 | 36.3824479839 | 5.80480112787 | 18 | 1.95853588581 | -0.0616694184817 | 0.302053443474 | 0.00485249508013 | -0.0155137619306 | 0.851626227574 | -0.0605714097201 | 0.0994948515423 | 0.0529569863466 | 0.241200175603 | 0.0746618053365 | 0.340245720524 | -0.0880054577448 | -0.0545785063002 | -0.00614338921291 | 0.126738330557 | 0.0314028255437 | 0.0270619169079 | 0.0985454351857 | 0.00130158951697 | 0.283136209876 | -2.08916714955 | 48.714758265 | 12.1021687734 | 19 | 0.885210429198 | 0.0526037333198 | -0.110602902217 | 0.821703349333 | 0.0348595375415 | 0.434309036818 | -0.0760646231971 | 0.247849558999 | -0.0816268915865 | -0.0945724992763 | 0.0502311671773 | 0.436242344248 | -0.122551663656 | 0.00933940207676 | 0.00713380850767 | 0.04579122682 | 0.0506960848196 | -0.0224788941254 | 0.0582295755737 | 0.000800340307682 | 0.248963210928 | 2.44703132296 | 36.3091718707 | 3.65635538291 |
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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 |
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1 | 1 | chain 'B' and (resid 343 through 371 )BF343 - 371 | 342 - 370 | 2 | 2 | chain 'B' and (resid 372 through 437 )BF372 - 437 | 371 - 436 | 3 | 3 | chain 'B' and (resid 438 through 467 )BF438 - 467 | 437 - 466 | 4 | 4 | chain 'C' and (resid 2 through 75 )CH2 - 75 | 1 - 74 | 5 | 5 | chain 'C' and (resid 76 through 141 )CH76 - 141 | 75 - 140 | 6 | 6 | chain 'C' and (resid 142 through 341 )CH142 - 341 | 141 - 340 | 7 | 7 | chain 'C' and (resid 342 through 423 )CH342 - 423 | 341 - 415 | 8 | 8 | chain 'C' and (resid 424 through 466 )CH424 - 466 | 416 - 458 | 9 | 9 | chain 'D' and (resid 2 through 99 )DJ2 - 99 | 1 - 98 | 10 | 10 | chain 'D' and (resid 100 through 155 )DJ100 - 155 | 99 - 154 | 11 | 11 | chain 'D' and (resid 156 through 371 )DJ156 - 371 | 155 - 370 | 12 | 12 | chain ' | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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