Software Name Version Classification PHENIX1.17.1_3660refinement XDSdata reduction Aimlessdata scaling PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 1.37→47.73 Å / SU ML : 0.1167 / Cross valid method : FREE R-VALUE / σ(F) : 1.91 / Phase error : 16.3887 Stereochemistry target values : GeoStd + Monomer Library + CDL v1.2Rfactor Num. reflection % reflection Rfree 0.1683 9712 5.02 % Rwork 0.1449 183918 - obs 0.1461 193630 99.94 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso mean : 18.72 Å2 Refinement step Cycle : LAST / Resolution : 1.37→47.73 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 3886 0 6 685 4577
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.0122 4287 X-RAY DIFFRACTION f_angle_d1.3196 5865 X-RAY DIFFRACTION f_chiral_restr0.099 648 X-RAY DIFFRACTION f_plane_restr0.0081 769 X-RAY DIFFRACTION f_dihedral_angle_d17.983 1621
LS refinement shell Show large table (7 x 30) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.37-1.39 0.2835 299 0.2615 6142 X-RAY DIFFRACTION 99.61 1.39-1.4 0.2348 293 0.2324 6141 X-RAY DIFFRACTION 99.67 1.4-1.42 0.226 299 0.2201 6234 X-RAY DIFFRACTION 99.86 1.42-1.44 0.2315 336 0.2087 6034 X-RAY DIFFRACTION 99.8 1.44-1.46 0.2156 327 0.2048 6159 X-RAY DIFFRACTION 99.86 1.46-1.48 0.2253 333 0.1885 6126 X-RAY DIFFRACTION 99.95 1.48-1.5 0.2257 320 0.1816 6084 X-RAY DIFFRACTION 99.95 1.5-1.52 0.2035 378 0.1753 6062 X-RAY DIFFRACTION 99.97 1.52-1.54 0.1718 375 0.1701 6194 X-RAY DIFFRACTION 99.97 1.54-1.57 0.1858 300 0.1655 6044 X-RAY DIFFRACTION 99.95 1.57-1.6 0.1883 357 0.1571 6127 X-RAY DIFFRACTION 99.95 1.6-1.62 0.1827 332 0.1571 6130 X-RAY DIFFRACTION 100 1.62-1.66 0.1766 297 0.1458 6174 X-RAY DIFFRACTION 99.97 1.66-1.69 0.1788 319 0.15 6126 X-RAY DIFFRACTION 99.98 1.69-1.73 0.1735 306 0.1486 6151 X-RAY DIFFRACTION 99.97 1.73-1.77 0.1761 331 0.1446 6164 X-RAY DIFFRACTION 100 1.77-1.81 0.1643 298 0.1423 6086 X-RAY DIFFRACTION 99.95 1.81-1.86 0.1461 323 0.1378 6148 X-RAY DIFFRACTION 100 1.86-1.91 0.1814 285 0.1407 6205 X-RAY DIFFRACTION 99.94 1.91-1.98 0.1538 321 0.1367 6131 X-RAY DIFFRACTION 100 1.98-2.05 0.1386 321 0.1318 6112 X-RAY DIFFRACTION 100 2.05-2.13 0.1542 356 0.1325 6080 X-RAY DIFFRACTION 100 2.13-2.23 0.148 299 0.1361 6155 X-RAY DIFFRACTION 100 2.23-2.34 0.1585 317 0.1316 6122 X-RAY DIFFRACTION 99.98 2.34-2.49 0.1618 365 0.1377 6150 X-RAY DIFFRACTION 100 2.49-2.68 0.164 314 0.1375 6120 X-RAY DIFFRACTION 100 2.68-2.95 0.182 336 0.1479 6128 X-RAY DIFFRACTION 100 2.95-3.38 0.163 314 0.1375 6137 X-RAY DIFFRACTION 99.98 3.38-4.26 0.1364 298 0.1211 6153 X-RAY DIFFRACTION 99.98 4.26-47.73 0.1698 363 0.1393 6099 X-RAY DIFFRACTION 99.92
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 15) 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 0.165638883842 -0.14269647126 -0.111930353127 0.18348296399 0.0235545591249 0.0750287776435 0.0525292858788 0.0373938981996 -0.0158622554953 -0.0485337745457 -0.0256532168179 -0.0123366534191 0.0514456831153 0.0546355715481 -1.2227517648E-5 0.179716283564 -0.00631488258172 -0.000815726994236 0.14718767708 -0.00741800577994 0.154971271824 -2.88943763233 -3.81017749641 14.5525669973 2 0.152172151786 0.0123105591992 -0.0123132205018 0.0367190009444 -0.0133457971196 0.0173749132623 0.0227095923489 0.00201699819531 -0.0946669426081 -0.0364026165649 0.00414370735923 0.0844195553934 -0.0141041382191 -0.0276095284669 -6.16691105934E-5 0.10623943383 -0.000771451599497 -0.000647640546992 0.111590804163 -0.00242932677962 0.127214384936 -5.04599478177 9.92571505597 32.1448513517 3 0.0567252984243 0.102988227507 0.0529468591574 0.118948350307 0.00328735885231 0.177191780009 -0.0490412725451 0.0366341515207 -0.0784743620042 0.066491194771 -0.00289687379243 0.125002685694 0.0668930010553 -0.142337597647 -0.000751886775411 0.113295617907 -0.00954274122798 0.00283940026474 0.148182408343 -0.0178553498629 0.138426906555 -8.9231322298 10.9583301469 17.3367483342 4 0.0854887432617 -0.089745826057 -0.0506122626443 0.136988037057 -0.0542804671633 0.204507723575 -0.00176536251805 -0.0224763252373 0.00498474815232 0.00560146299091 0.0100598656868 -0.0187902104034 -0.072742080494 0.00810232042674 2.06859400912E-6 0.108120917804 -0.00750589551473 0.00853610947131 0.100531113131 -0.0084587642946 0.0939337326903 4.61541286025 20.0043453307 19.3881436398 5 0.0799677740642 -0.0117170868762 -0.00816658705509 0.0601149263929 -0.133705449919 0.197898232704 0.0145395947003 0.0620174590817 0.100365764957 -0.140506421268 0.030372927416 0.0250933595759 -0.156225925455 -0.103283475443 4.1440163414E-5 0.161843518986 0.0134436411462 -0.00172291244562 0.158229758765 -0.00117109131545 0.135778586902 -3.64238000631 21.7311694675 10.3079010946 6 0.252473515975 0.156358880667 0.205217272795 0.459831870383 0.00496095485345 0.386862106179 0.0225514946833 0.202137528522 0.0887378433384 -0.232137769655 -0.0167975904314 0.0348767543458 -0.189087117372 0.0117738056915 -0.136088451697 0.17409450757 -0.00675062022144 0.0223188831178 0.162588523908 0.0113528752115 0.110018320499 5.5869693952 21.7207998589 4.06847915092 7 0.309717285891 -0.0617855225017 0.177167305218 0.17006344039 0.146679574841 0.366271452322 -0.0402718327186 0.179491431067 0.0661932650863 -0.16584430702 0.0332851349697 -0.0201149019148 -0.0776661294436 0.079466080067 -0.00479469334089 0.152393782227 -0.0277696326801 0.0272918519687 0.151402121504 0.00365418417428 0.122216180495 13.8019095853 16.5514182258 8.61830801405 8 0.35287897737 -0.147770747185 0.152705688285 0.0689399311199 -0.0540944889515 0.215246655911 0.00240211963903 0.080272737071 -0.0850709646482 -0.0478466846647 0.0380845911275 -0.0386205677208 0.0239337194391 0.0448838707833 0.000494812287251 0.117816864478 -0.00561098409014 0.010792596055 0.108245515114 -0.0143684342351 0.125910211113 9.76969312094 1.83978376361 16.2332671967 9 0.0599682449809 0.0537215685052 -0.0349454154081 0.039153917862 0.000701827362556 0.045949059625 -0.0276164780996 0.137669366233 -0.122932467258 -0.09418970708 0.0319111171121 -0.0898474067766 0.0616804686087 0.0695243003314 -0.000885355135125 0.151744595176 -0.0075254738156 0.0360940090939 0.135446089637 -0.0244836738595 0.142873132098 12.7649948378 -1.52900572832 11.8551359428 10 0.119106837063 -0.134364431156 0.0408452377554 0.0981585405591 -0.0703668296825 0.11951304984 -0.0110149227545 0.0811463215487 -0.0521661661189 -0.0138164907209 -0.0133438459194 -0.080171008728 0.0288460372257 0.040361348651 0.000386089497294 0.106819351589 -0.0112553290334 0.0166947986232 0.122965733505 -0.00344580302207 0.12318914345 18.0405575864 11.1946216803 19.3434625067 11 0.00573017793385 0.028386568824 -0.05195796966 0.10459308286 -0.020244489875 0.0675376767256 -0.01431952261 -0.132379937922 -0.0549699336564 0.0808127568856 0.0749108615651 -0.00816940000548 0.19008648443 0.10506825338 -9.97725870428E-5 0.190478392592 0.0131285014842 -0.0106948945244 0.199268357496 0.0242084699656 0.19736069032 11.4287429393 -4.98230993876 45.4140712004 12 0.0597093987554 0.0171895949329 0.0340890643023 0.0395416609101 -0.00766987797479 0.0973213160396 -0.0046568898666 -0.0681202846147 -0.0922741866508 -0.00955599697743 0.0202146677341 -0.0295259224204 0.0631518057243 0.037022588554 1.80755432006E-5 0.129145992847 0.00125674020561 0.00254601383115 0.130472975672 0.00200244897924 0.145178454342 19.5744643202 -0.736043050852 26.307590075 13 0.322476812552 0.0791254354442 -0.0488051201287 0.252481052295 0.227160331874 0.595244986041 -0.00360422908843 -0.00290427855216 -0.0166254941199 0.0106002121682 0.00272826119745 -0.0267846950145 0.0295561434217 0.039241076963 -9.27459959052E-6 0.102408741004 0.00058497336173 0.0057322719967 0.106270471963 0.00182655845441 0.108456765436 22.1955852877 9.7387729794 36.867688878 14 0.33651653167 -0.208638205179 0.138773530643 0.245438730228 0.0532359522671 0.476220405218 -0.0157326381089 -0.0961881147755 0.120187817245 0.0387432201941 0.00686884260707 -0.106894981298 -0.0975212952499 0.0891587564541 -0.000405677610224 0.118453055182 -0.016212062394 -0.00603049720065 0.129261084283 -0.00903313211172 0.137368531076 23.7149723129 19.0922324032 44.9030558072 15 0.449048773035 0.0557285741619 0.148170202703 0.330083870267 -0.00786185760708 0.246369867368 0.0087204755262 -0.058556411687 -0.0117826668437 0.0357611814219 -0.00728498622476 -0.00470541814051 -0.00145845601052 -0.0355530271316 -3.01715255802E-6 0.115122823911 0.00146748503792 0.00611263682523 0.102542800923 -0.00177646865172 0.0999441939469 4.44377692417 13.3872183762 42.2820742136
Refinement TLS group ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid -2 through 18 ) 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 19 through 35 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 36 through 56 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 57 through 92 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 93 through 118 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 119 through 142 )7 X-RAY DIFFRACTION 7 chain 'A' and (resid 143 through 171 )8 X-RAY DIFFRACTION 8 chain 'A' and (resid 172 through 198 )9 X-RAY DIFFRACTION 9 chain 'A' and (resid 199 through 217 )10 X-RAY DIFFRACTION 10 chain 'A' and (resid 218 through 239 )11 X-RAY DIFFRACTION 11 chain 'B' and (resid -2 through 18 ) 12 X-RAY DIFFRACTION 12 chain 'B' and (resid 19 through 35 )13 X-RAY DIFFRACTION 13 chain 'B' and (resid 36 through 92 )14 X-RAY DIFFRACTION 14 chain 'B' and (resid 93 through 157 )15 X-RAY DIFFRACTION 15 chain 'B' and (resid 158 through 239 )