Software | Name | Version | Classification |
---|
DIALS | | data scalingDIALS | | data reductionPHASER | | phasingPHENIX | 1.20.1_4487refinement | | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→43.09 Å / SU ML: 0.4524 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9231 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.2217 | 1319 | 4.97 % |
---|
Rwork | 0.1825 | 25211 | - |
---|
obs | 0.1845 | 26530 | 98.82 % |
---|
|
---|
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
---|
Displacement parameters | Biso mean: 57.49 Å2 |
---|
Refinement step | Cycle: LAST / Resolution: 2.64→43.09 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 1628 | 3262 | 0 | 201 | 5091 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
---|
X-RAY DIFFRACTION | f_bond_d0.0031 | 5288 | X-RAY DIFFRACTION | f_angle_d0.739 | 7894 | X-RAY DIFFRACTION | f_chiral_restr0.0426 | 1032 | X-RAY DIFFRACTION | f_plane_restr0.0048 | 430 | X-RAY DIFFRACTION | f_dihedral_angle_d13.5684 | 2046 | | | | | |
|
---|
Refine LS restraints NCS | Ens-ID | Dom-ID | Asym-ID | Auth asym-ID | Refine-ID | Type | Rms dev position (Å) |
---|
ens_1d_2DAX-RAY DIFFRACTION | Torsion NCS0.668569009287 | ens_2d_2ACX-RAY DIFFRACTION | Torsion NCS0.805739687209 | | | | | | | | | | |
|
---|
LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
---|
2.64-2.75 | 0.3978 | 151 | 0.3792 | 2780 | X-RAY DIFFRACTION | 99.29 | 2.75-2.87 | 0.3877 | 155 | 0.312 | 2781 | X-RAY DIFFRACTION | 99.16 | 2.87-3.02 | 0.3455 | 137 | 0.2515 | 2771 | X-RAY DIFFRACTION | 98.88 | 3.02-3.21 | 0.2898 | 145 | 0.2347 | 2755 | X-RAY DIFFRACTION | 97.84 | 3.21-3.46 | 0.2636 | 133 | 0.2135 | 2821 | X-RAY DIFFRACTION | 99.56 | 3.46-3.81 | 0.2345 | 148 | 0.1683 | 2823 | X-RAY DIFFRACTION | 99.5 | 3.81-4.36 | 0.1869 | 141 | 0.153 | 2801 | X-RAY DIFFRACTION | 99.16 | 4.36-5.49 | 0.1706 | 148 | 0.1347 | 2818 | X-RAY DIFFRACTION | 97.98 | 5.49-43.09 | 0.1568 | 161 | 0.1486 | 2861 | X-RAY DIFFRACTION | 98.12 |
|
---|
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 | 7.46506630477 | 0.0356711864404 | 0.861266037928 | 8.86737221059 | 0.541269938099 | 2.82850416474 | -0.384476139741 | -0.00553727843196 | -0.0918952700299 | -0.106728389141 | -0.165132511581 | -0.409422841277 | 0.508972869118 | 0.44121291806 | 0.481216843445 | 0.253964326089 | 0.0233897994522 | 0.0106037313361 | 0.284146389839 | -0.000231334725985 | 0.404165250659 | 45.9967293816 | -40.2811479142 | -21.0922837625 | 2 | 8.87826871497 | 4.71499530761 | -4.36043115212 | 7.25740298119 | -6.07950586115 | 6.80407885163 | -0.411057554781 | 0.377591672047 | 0.383136307799 | -0.516303518442 | 1.18533869173 | 1.02787484649 | -0.317613379116 | -0.663052238133 | -0.342486721264 | 0.374786277236 | -0.0142075667893 | 0.0229352641432 | 0.427649368263 | -0.0862963272814 | 0.456237834446 | 27.9526215471 | -42.3961413271 | -24.689039405 | 3 | 6.82060210013 | 4.46955227421 | 0.467412888507 | 7.94236290481 | 4.08029985784 | 5.23132429248 | 0.0739311561697 | 0.202280310251 | 0.246220554389 | 0.378345158133 | 0.257119687855 | 0.0979082747823 | -0.43555458413 | 0.0199866818593 | -0.282010062592 | 0.435638443067 | 0.0192306283697 | 0.015452179734 | 0.307881410677 | 0.0809374930718 | 0.385286753646 | 44.2256547453 | -24.4891106493 | -19.9824528351 | 4 | 2.01773187051 | -1.0280770357 | -1.52073400084 | 4.59587725823 | -3.73290924263 | 4.33780552536 | -0.306753211009 | -1.50921079029 | 0.743447165336 | 1.63544104608 | -0.503064270371 | -0.614829694607 | -0.861457442607 | -0.766300137689 | 0.751694493117 | 0.495480829532 | -0.0552808401653 | -0.0983476069333 | 0.553469494934 | -0.0521828597866 | 0.396609723956 | 40.6130864679 | -20.1816675999 | -3.73933068063 | 5 | 2.39330565893 | -1.56766239086 | -2.40858289527 | 3.10145091085 | 3.01594228106 | 3.42767538466 | -0.135992386679 | -0.288418828109 | -0.0416995730965 | -0.290390269656 | -0.310875366219 | 0.160904687936 | -1.33618060614 | -0.594086281383 | 0.645335151881 | 0.45908959262 | 0.0349810360713 | -0.099580604579 | 0.444120470474 | 0.0173443180024 | 0.500314992722 | 42.6389591296 | -21.3543156907 | -17.8988003203 | 6 | 4.6141061187 | -4.37893746515 | -4.95129279608 | 8.55792843851 | 5.51028842054 | 5.63228057056 | 0.474394189743 | 0.569763552052 | 0.534765203156 | -0.994602317619 | -0.577947709777 | 0.649756953858 | -2.25094246712 | -0.643840223803 | 0.0830806415517 | 0.558947692516 | 0.0686704308472 | -0.0850671266714 | 0.600317131712 | 0.0261882923521 | 0.604767558222 | 38.806864041 | -22.4298613207 | -23.8094679748 | 7 | 0.924617899156 | -0.322711491542 | -1.59935877349 | 2.98819332071 | 1.10175282432 | 3.77327946627 | -0.149058476058 | 0.0317813175955 | 0.46494709194 | -0.0384984961547 | -0.0507095934205 | 0.102882114245 | -0.179469339971 | 0.379858326954 | 0.122306927026 | 0.270990394171 | 0.0114559450621 | -0.0724357009954 | 0.30899957369 | -0.035171811657 | 0.522410321061 | 43.7607675272 | -27.8678325106 | -15.4350504366 | 8 | 4.51064639566 | 5.17361089862 | 4.06463798832 | 9.39080578304 | 5.19458161629 | 3.88987196844 | -0.0554438714317 | 0.264974185711 | 0.666118933318 | -0.294967795483 | 0.0171383576016 | 0.393419772775 | -0.72412742747 | 0.0104593859192 | 0.168166454647 | 0.361283574874 | 0.0895415576712 | -0.0213509606567 | 0.483306103357 | -0.0956439575548 | 0.506397119432 | 32.2895020286 | -20.198393697 | -13.5253597225 | 9 | 6.92739880244 | 2.30030265599 | -2.28607091145 | 6.32999428377 | -4.92287731104 | 3.85961982932 | -0.384294835298 | -0.628720723869 | -0.562892149966 | 0.631888449526 | -0.894602522885 | 0.404129252952 | 1.04424884657 | -0.0154332604915 | 1.30012836499 | 0.625293241104 | 0.0958156041012 | 0.1491693622 | 0.295733315047 | -0.0988604350229 | 0.538377285153 | 39.6841959346 | -34.1259914079 | -14.1257737057 | 10 | 8.1096573324 | 0.43140359336 | -1.5940213907 | 8.47428346648 | 0.437499337899 | 9.07954163578 | -0.100657714073 | 0.260015829456 | 0.139269162743 | -0.0587925460092 | 0.119140122296 | 0.002786431246 | 0.0218796197872 | 0.571756821466 | -0.051795575267 | 0.173983376381 | 0.0268541361972 | -0.0283448755249 | 0.305795001959 | -0.0285661096034 | 0.392913827033 | 46.1249692034 | -36.2666904667 | -21.3033325598 | 11 | 2.3249750327 | -0.454557675912 | 1.6732251772 | 3.47297622964 | -0.00718534625261 | 1.51323288775 | -0.104566415756 | -0.112987067706 | -0.319580259369 | 0.104911393717 | 0.195953270805 | 0.136723252003 | 0.14590506576 | -0.214185417238 | -0.0202530101558 | 0.359188396799 | 0.0418602557699 | 0.0712240279713 | 0.418343137706 | -0.0526407117618 | 0.479004356548 | 17.7863348209 | 16.5911066983 | 4.70100838789 | 12 | 0.652261862167 | 0.129306004662 | 0.703673540115 | -0.119574620335 | 0.326318010727 | -0.498242778965 | -0.431145893227 | -1.20917062572 | 0.952498268184 | 0.118424968214 | 0.289727981002 | -0.130936552762 | 0.027674253393 | -0.356520233603 | 0.196436204912 | 0.41916813572 | 0.118609672421 | 0.00872378511384 | 0.904979070804 | -0.135526296858 | 0.880714579703 | 1.71810386298 | 26.47659727 | 10.8801281829 | 13 | 0.187366373215 | 0.268915662734 | -0.563124395194 | 8.27302194271 | 0.638578361743 | 0.342358785298 | 0.120614526437 | 0.0134062046998 | -0.211676232192 | 0.228277633579 | -0.305266038153 | 0.0216672825709 | 0.0871411846025 | -0.0500692179981 | 0.172154413556 | 0.383382842347 | -0.0218051679174 | -0.0336777256782 | 0.487806509088 | -0.0701831066808 | 0.564038848314 | 31.7135411036 | 4.75352478487 | 5.12382509957 | 14 | 2.73901788912 | -0.0223973709351 | -1.72616566882 | 2.03901778256 | -0.458986793029 | 2.0379284246 | -0.237675195438 | 0.0311510017917 | 0.0299145730086 | -0.218469721151 | 0.381494088384 | 0.237411153623 | -0.235245374377 | -0.492419709817 | 0.00377569789556 | 0.41753581269 | -0.053377228557 | -0.08464740706 | 0.442658511673 | -0.0360745158877 | 0.541540589385 | 21.9309375539 | -93.8196152329 | -47.9258055426 | 15 | 1.5531912283 | -0.180562894526 | -1.01547926107 | -0.0886716976314 | 0.506357331047 | -0.402273594477 | -0.417060864558 | 1.29920213822 | -1.15092922165 | -0.15657649653 | 0.224971190626 | -0.0822902509808 | -0.120404518347 | -0.319083639526 | 0.189966347626 | 0.455457974921 | -0.155472806619 | 0.0584192368147 | 0.898012997385 | -0.131081095509 | 0.846548166574 | 5.35082767431 | -103.642139707 | -54.3972303122 | 16 | 0.30364380546 | 0.669721702041 | 0.811726469832 | 7.50809181603 | 0.0163750875954 | 0.207980744076 | -0.00431484941084 | 0.0906363091965 | 0.219086620345 | -0.201790348396 | -0.228339102908 | -0.269577256909 | -0.161594867582 | 0.0210234937863 | 0.198741475941 | 0.483577618766 | -0.0105894416145 | 0.127242627398 | 0.465362027149 | -0.0478839764043 | 0.556521491746 | 35.9768349045 | -83.1161219909 | -48.535207242 | 17 | 3.46978699848 | 0.935202170603 | -0.262804194638 | 4.32902296534 | -6.24220554291 | 9.4018557473 | -0.402306645213 | -0.458747266633 | -0.00698743677659 | -0.554432682793 | 0.654647913221 | 0.558303438745 | 0.479487169089 | -1.31661410846 | -0.0584958456459 | 0.373588346554 | 3.93077241387E-5 | 0.0284272908033 | 0.483894185356 | -0.0782259723483 | 0.555409948302 | 27.412621749 | -36.1911101787 | -18.6183339846 | 18 | 2.74106113109 | 0.366589962187 | 1.97954862595 | 4.42619241581 | 1.77249088976 | 7.20662127176 | 0.0843841000462 | 0.395974789722 | -0.597237411846 | 0.109482657816 | 0.309847613688 | -0.454512702641 | 1.26386270699 | 0.770691476297 | -0.458346033992 | 0.348346340963 | 0.0590725484595 | -0.0373812713649 | 0.307144905822 | -0.0692003743962 | 0.512232653868 | 45.208827198 | -54.0440824757 | -27.8045475482 | 19 | 1.40180930801 | 0.538772885737 | -0.199288211967 | 1.80519990106 | 1.62856498105 | 6.65818498942 | -0.0574215153756 | -0.0965321228517 | -0.131552371768 | 0.216253889161 | -0.0284547896598 | -0.276583605014 | 0.514447985604 | 0.217238639514 | 0.0910096018665 | 0.427310712324 | 0.0634175030557 | 0.0318516707574 | 0.404517530737 | -0.0648844998183 | 0.682843998292 | 45.8377037503 | -51.5148209191 | -24.0580598077 | 20 | 4.70328550257 | -4.87040272524 | -4.50647652259 | 5.24194821904 | 4.8146719728 | 4.79923958224 | 0.0604249408124 | 0.182305418533 | -0.926219331868 | 0.1025790059 | -0.507546485641 | 1.06972155879 | 0.448228165638 | -0.903357511128 | 0.669582244719 | 0.547217204765 | -0.0155717802875 | 0.0675942483043 | 0.417496927004 | -0.0545596405238 | 0.586246666038 | 34.5000901541 | -53.8495532528 | -26.5928881898 |
|
---|
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 'B' and (resid 88 through 111 )BC88 - 111 | 84 - 107 | 2 | 2 | chain 'A' and (resid 5 through 16 )AD5 - 16 | 1 - 12 | 3 | 3 | chain 'A' and (resid 17 through 27 )AD17 - 27 | 13 - 23 | 4 | 4 | chain 'A' and (resid 28 through 34 )AD28 - 34 | 24 - 30 | 5 | 5 | chain 'A' and (resid 35 through 40 )AD35 - 40 | 31 - 36 | 6 | 6 | chain 'A' and (resid 41 through 50 )AD41 - 50 | 37 - 46 | 7 | 7 | chain 'A' and (resid 51 through 74 )AD51 - 74 | 47 - 70 | 8 | 8 | chain 'A' and (resid 75 through 84 )AD75 - 84 | 71 - 80 | 9 | 9 | chain 'A' and (resid 85 through 90 )AD85 - 90 | 81 - 86 | 10 | 10 | chain 'A' and (resid 91 through 111 )AD91 - 111 | 87 - 107 | 11 | 11 | chain 'C' and (resid 1 through 30 )CA1 - 30 | | 12 | 12 | chain ' | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
|
---|