Software | Name | Version | Classification |
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PHENIX | 1.20.1_4487refinementXDS | | data reductionautoPROC | | data processingSTARANISO | | data scalingAimless | | data scalingPHASER | | phasing | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→62.76 Å / SU ML: 0.2497 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7338 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2241 | 2000 | 2.18 % |
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Rwork | 0.1768 | 89798 | - |
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obs | 0.1779 | 91798 | 67.27 % |
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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: 37.76 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.96→62.76 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 14742 | 0 | 108 | 1192 | 16042 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.0067 | 15450 | X-RAY DIFFRACTION | f_angle_d0.8519 | 20899 | X-RAY DIFFRACTION | f_chiral_restr0.0536 | 2241 | X-RAY DIFFRACTION | f_plane_restr0.007 | 2727 | X-RAY DIFFRACTION | f_dihedral_angle_d12.9109 | 5854 | | | | | |
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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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1.96-2.01 | 0.3067 | 8 | 0.2734 | 325 | X-RAY DIFFRACTION | 3.46 | 2.01-2.07 | 0.2973 | 33 | 0.2651 | 1500 | X-RAY DIFFRACTION | 16.01 | 2.07-2.13 | 0.3377 | 52 | 0.2583 | 2377 | X-RAY DIFFRACTION | 25.22 | 2.13-2.2 | 0.333 | 74 | 0.2434 | 3303 | X-RAY DIFFRACTION | 34.84 | 2.2-2.28 | 0.2654 | 102 | 0.236 | 4569 | X-RAY DIFFRACTION | 48.52 | 2.28-2.37 | 0.3062 | 130 | 0.2212 | 5837 | X-RAY DIFFRACTION | 61.67 | 2.37-2.48 | 0.2725 | 154 | 0.2236 | 6891 | X-RAY DIFFRACTION | 72.95 | 2.48-2.61 | 0.2692 | 174 | 0.218 | 7869 | X-RAY DIFFRACTION | 82.75 | 2.61-2.77 | 0.2613 | 199 | 0.2157 | 8895 | X-RAY DIFFRACTION | 93.41 | 2.77-2.98 | 0.2733 | 211 | 0.2008 | 9452 | X-RAY DIFFRACTION | 99.71 | 2.98-3.28 | 0.2645 | 212 | 0.185 | 9540 | X-RAY DIFFRACTION | 99.56 | 3.28-3.76 | 0.2329 | 212 | 0.1579 | 9560 | X-RAY DIFFRACTION | 99.42 | 3.76-4.73 | 0.1546 | 216 | 0.1357 | 9645 | X-RAY DIFFRACTION | 99.53 | 4.73-62.76 | 0.1858 | 223 | 0.1549 | 10035 | X-RAY DIFFRACTION | 99.87 |
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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 | 1.77532047307 | 0.686696959952 | 0.41980235265 | 1.3871165611 | 0.479415261525 | 1.07866818528 | -0.162159790122 | 0.310154859825 | 0.239930691322 | -0.256871967088 | 0.0923515085714 | -0.0384782065333 | -0.224815037559 | 0.0434104354642 | 0.0579432133068 | 0.202929268422 | -0.0232313168975 | -0.0127055273278 | 0.175890465492 | 0.011588121984 | 0.201248172724 | 36.6958677617 | 43.8580754304 | 8.02361992466 | 2 | 0.858959019033 | -0.172150373362 | 0.193810598371 | 2.76198687375 | -0.105741013872 | 1.14906208974 | 0.0588572021573 | -0.212104710091 | 0.200542923636 | 0.294906364632 | -0.111293540902 | 0.248848911823 | -0.00278652268769 | -0.133210450986 | 0.047441113814 | 0.190115626686 | -0.0336190337994 | 0.0218401494199 | 0.266464180384 | -0.098802093131 | 0.20768103001 | 20.4179315622 | 50.0269990933 | 30.5468314748 | 3 | 0.663332519387 | 0.0301477633756 | 0.13218987513 | 1.33924810282 | 0.354228694335 | 0.958513162972 | 0.0737433776565 | -0.350883399028 | 0.448972225328 | 0.141675516867 | -0.0800278310157 | 0.0306169728442 | -0.200459379594 | 0.0499206502338 | 0.0128967486631 | 0.313493940126 | -0.0635660249521 | 0.00344284106 | 0.277107725686 | -0.149875153597 | 0.275109412457 | 29.9688692958 | 56.7108375838 | 31.5047145031 | 4 | 1.31380181089 | 0.774131974968 | -0.396149299755 | 0.834944801178 | -0.365506937426 | 0.253976373326 | 0.0108264816662 | -0.128912009668 | 0.453823368327 | 0.0335135821942 | -0.00230133140791 | 0.0448447088086 | -0.195260343306 | 0.00133389087473 | -0.00868150361906 | 0.278762781368 | -0.0403681179741 | -0.0256450507801 | 0.166828976883 | -0.0744053509667 | 0.32396393382 | 39.2273209582 | 52.4738543867 | 18.2739865311 | 5 | 0.912100432973 | 0.0289171074879 | 0.842144163783 | 1.99776549405 | -1.11784342842 | 2.07906721617 | -0.306944353174 | -0.239448566628 | 0.867842898689 | 0.0294412731007 | 0.135481809421 | 0.156402766891 | -0.370848066486 | -0.192123781686 | 0.0561523277102 | 0.22332033428 | -0.0112776992187 | -0.0322729176593 | 0.207396351239 | -0.054223958642 | 0.581276335069 | 37.8801398544 | 59.8183710869 | 9.15864258988 | 6 | 6.54851775813 | 1.40504139469 | 0.278187812696 | 1.26120630408 | 0.624229777427 | 0.757741699977 | -0.109645370819 | 0.42791291747 | 1.08984754492 | -0.25679386671 | -0.0905280766151 | 0.594049841448 | -0.290494304365 | -0.386067180425 | 0.0863139462616 | 0.643410431705 | -0.0797075158096 | -0.099121851159 | 0.318592114558 | 0.112266605458 | 0.889740697293 | 30.3305979335 | 66.4655021951 | 1.82222891094 | 7 | 1.22498707279 | 0.0714579824978 | -0.107366569945 | 1.14927997814 | -0.0111352684825 | 0.303246234229 | 0.0132776589696 | 0.0820378568184 | 0.131462025244 | 0.0159380504683 | -0.0253406150794 | 0.142436234769 | -0.0498259311295 | -0.0652819270918 | 0.00882886742597 | 0.115281677362 | -0.00701692083974 | 0.00186176628554 | 0.145095395538 | -0.00709016667213 | 0.111750184418 | 6.09945871886 | 35.8124219123 | 8.67299833844 | 8 | 0.937156465985 | 0.119222262084 | 0.494752175186 | 0.881473062004 | 0.320178008329 | 1.86350751121 | 0.0277536193793 | -0.775192689389 | 0.589094658682 | 0.38718610716 | -0.328712344723 | 0.870827363468 | -0.116373679222 | -0.538356436684 | 0.0813233862162 | 0.288641769606 | -0.0294866650896 | 0.160728341004 | 0.455438984478 | -0.235960748911 | 0.646472698457 | -2.14457404757 | 26.4283025006 | 26.3200781634 | 9 | 1.78836532632 | 0.213964960368 | -0.363864300465 | 1.00840538569 | -0.00933405419645 | 0.467925053017 | 0.0413338780378 | -0.0204680849985 | -0.0776948339341 | -0.0290217130707 | -0.0720507703701 | -0.200791203798 | 0.0226661443007 | 0.0515187817447 | 0.0132132603596 | 0.132610902931 | -0.00644638129227 | 0.0080956802871 | 0.145507226069 | 0.0529768610104 | 0.129531361613 | 55.5307439286 | 19.3829868137 | -2.6066548722 | 10 | 1.18501385863 | 0.340873729861 | -0.21623897342 | 1.19805392977 | -0.648441638524 | 0.75903896694 | 0.0431440576853 | -0.836246160184 | -0.886226628582 | -0.142742061743 | -0.552812460398 | -1.20166749762 | 0.246965170363 | 0.932413435883 | -0.0191436868537 | -0.0247643195945 | -0.0522377895725 | -0.0656191015017 | 0.552793952289 | 0.309479525008 | 0.942454607345 | 69.7038289299 | 23.6585613608 | 14.8824797093 | 11 | 1.31563050692 | 0.563433257115 | 0.0455123090389 | 2.06359753936 | -0.0749352168034 | 0.413433946744 | 0.010156149951 | -0.0730394233711 | -0.20309380875 | 0.0689914790685 | -0.0582528423271 | -0.209104338232 | 0.0626276915528 | 0.0353853617328 | 0.0323061103588 | 0.173841184788 | -0.0294312620042 | -0.0264841537245 | 0.138333102865 | 0.0467500888281 | 0.0814606935905 | 36.7041680889 | -1.32394240002 | 15.6737394756 | 12 | 0.971935174358 | 0.718280958645 | -0.604923233278 | 0.98435171404 | -0.260436637187 | 2.20084792472 | -0.550617595468 | 0.412740643261 | -0.547542196551 | -0.898318727039 | 0.295757970748 | -0.437543909264 | 0.68770008738 | -0.0394441099418 | 0.057753504714 | 0.559242847356 | -0.110009335902 | 0.166113542317 | 0.25168978635 | -0.08186692373 | 0.383928632702 | 25.0378652053 | -8.04142230101 | -1.95671352469 |
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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 'A' and (resid 2 through 75 )AA2 - 75 | 1 - 74 | 2 | 2 | chain 'A' and (resid 76 through 132 )AA76 - 132 | 75 - 131 | 3 | 3 | chain 'A' and (resid 133 through 295 )AA133 - 295 | 132 - 294 | 4 | 4 | chain 'A' and (resid 296 through 371 )AA296 - 371 | 295 - 370 | 5 | 5 | chain 'A' and (resid 372 through 437 )AA372 - 437 | 371 - 436 | 6 | 6 | chain 'A' and (resid 438 through 467 )AA438 - 467 | 437 - 466 | 7 | 7 | chain 'B' and (resid 2 through 341 )BD2 - 341 | 1 - 340 | 8 | 8 | chain 'B' and (resid 342 through 467 )BD342 - 467 | 341 - 466 | 9 | 9 | chain 'C' and (resid 2 through 342 )CH2 - 342 | 1 - 341 | 10 | 10 | chain 'C' and (resid 343 through 466 )CH343 - 466 | 342 - 465 | 11 | 11 | chain 'D' and (resid 2 through 341 )DK2 - 341 | 1 - 340 | 12 | 12 | chain 'D | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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