ソフトウェア 名称 バージョン 分類 PHENIX1.15_3448精密化 HKL-3000データ削減 HKL-3000データスケーリング PHENIX位相決定
精密化 構造決定の手法 : 分子置換開始モデル : 5fr7解像度 : 2.59→29.93 Å / SU ML : 0.4054 / 交差検証法 : FREE R-VALUE / σ(F) : 1.34 / 位相誤差 : 29.9029 立体化学のターゲット値 : GeoStd + Monomer Library + CDL v1.2Rfactor 反射数 %反射 Selection details Rfree 0.2946 984 5.01 % RANDOM Rwork 0.2375 18639 - - obs 0.2403 19623 99.3 % -
溶媒の処理 減衰半径 : 0.9 Å / VDWプローブ半径 : 1.11 Å / 溶媒モデル : FLAT BULK SOLVENT MODEL原子変位パラメータ Biso mean : 48.61 Å2 精密化ステップ サイクル : LAST / 解像度 : 2.59→29.93 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 4364 0 2 32 4398
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.0029 4445 X-RAY DIFFRACTION f_angle_d0.596 6051 X-RAY DIFFRACTION f_chiral_restr0.0426 723 X-RAY DIFFRACTION f_plane_restr0.0034 782 X-RAY DIFFRACTION f_dihedral_angle_d21.0767 1605
LS精密化 シェル 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.59-2.73 0.3851 137 0.3258 2591 X-RAY DIFFRACTION 96.88 2.73-2.9 0.3498 141 0.314 2634 X-RAY DIFFRACTION 99.78 2.9-3.12 0.3407 137 0.2958 2671 X-RAY DIFFRACTION 99.93 3.12-3.44 0.3394 142 0.2697 2676 X-RAY DIFFRACTION 99.96 3.44-3.93 0.2984 143 0.2259 2685 X-RAY DIFFRACTION 99.93 3.93-4.95 0.2614 142 0.1915 2693 X-RAY DIFFRACTION 99.65 4.95-29.93 0.2335 142 0.1988 2689 X-RAY DIFFRACTION 98.95
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 17) 大きな表を隠す 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 3.24986490819 2.30509771638 -3.33600140362 2.55956934245 -0.76683463314 6.32165847544 0.415502751965 -0.896950871315 0.272342644606 0.0990166290273 -0.407266850219 -0.118150987832 -0.486440650691 0.23934876649 0.128774019971 0.370932933062 -0.013090539259 -0.00236921910901 0.366274488584 0.00143272450525 0.344638456678 24.221990667 -6.67570019805 11.4770474291 2 8.55879303738 1.15598783115 -1.92225020489 6.39136610913 3.76635611637 3.11739749505 0.000585250480198 -0.16224416615 -0.420457542948 -0.0112145663981 -0.158522284373 0.297760300509 0.0895329193435 -0.0928138301349 0.289047103057 0.289990102139 -0.0241770628342 -0.00165549183549 0.382639742153 0.0395056497866 0.196358355639 11.844993564 -11.8960217194 15.030114027 3 6.58104244921 1.88280105365 2.30373115541 0.712462310869 -0.0177225849071 3.28049278329 0.235909283847 -0.0583204009983 0.213825223711 0.132311578542 -0.103536227587 0.00664002147172 0.169050564151 -0.360591435147 -0.159850205914 0.351078901282 0.0491065121101 0.00682444543183 0.274787551715 -0.0454681494676 0.285691877175 3.30057913782 -12.6728535533 1.17527980006 4 9.12596078065 4.68391892195 0.297233663264 2.85307323375 0.236011619304 1.27232238189 0.175278970127 0.0803255128237 0.0466797232441 0.0379381148849 -0.120804707078 0.0670416139047 -0.0236145119963 -0.151235251653 -0.0753248528668 0.32039755897 0.0484044079377 -0.0382106749658 0.313569120844 -0.0140896820529 0.24919267889 6.58965607475 -8.55494866073 1.89171765836 5 7.01826925398 3.27649989285 0.44760344173 5.7806129862 4.2492178552 7.81405109802 -0.373823459108 1.12206816676 0.537425294587 -0.55307277205 0.215124825488 0.381764950735 -0.67419596366 -0.195454679845 0.104616310039 0.400852555358 0.0406001320174 -0.0197009861767 0.368677193035 0.15325531866 0.427777862115 20.7250174426 0.707888709271 -19.4069807165 6 3.76901355658 1.95348522846 2.49172647357 1.82892260506 0.821061401221 2.90360857402 0.0205519107749 0.057485004452 -0.0363683902406 -0.135563296484 -0.00599066890512 0.0322026121314 0.0409959921507 0.0404490158116 0.00887352273328 0.295113073453 0.0520461130681 0.0682054161035 0.28294424164 -0.0180756071591 0.26332682695 11.5325086998 -10.4082513726 -15.1153711482 7 3.01617876148 -2.57985504769 4.4172505098 6.63186018047 -2.37218288093 6.92209338402 -0.274373782262 0.693136721079 -0.672215439826 -0.873881638727 0.674793900577 0.47577979316 0.372826239014 -0.226361342745 -0.302359562825 0.413303730156 -0.130768673046 -0.0240019719584 0.475436720919 -0.0742520624712 0.445915784337 18.7050302403 -32.7150316209 -36.664630335 8 6.29118380663 -3.02012872438 -5.88517817353 2.5922558903 2.9227266944 5.51746379209 -0.973029611735 -0.355713085371 1.69744691001 -0.125965271496 1.66394861321 -1.04572821489 1.89096156381 0.216839144929 -0.81971215456 0.555709556703 -0.0753612918405 -0.0727565277321 0.365470893457 0.0680547219563 0.663865414757 25.7751288406 -22.797500645 -41.3635222746 9 7.81779165893 2.15570480169 2.17406899779 1.50380996195 -1.25029975169 4.78930052236 -0.211931041067 0.284905932849 0.24079322267 -0.258026708224 0.117977770464 -0.105316931836 -0.184237369053 -0.15488180284 0.0916385795972 0.300496635896 0.00922542000663 0.0109997647176 0.313256249307 -0.0675868922051 0.212893907547 30.9147454526 -20.8731082296 -31.6101728583 10 4.33638597333 3.5800070559 1.40825455634 4.26726682677 0.0545239197408 1.36315440994 0.0260870863371 -0.0966393606441 -0.0653963710994 -0.00608705869142 -0.00143709564341 0.0293462927403 0.0194374166592 -0.0976687664402 -0.0169073229967 0.22032012862 0.0956106378402 -0.0360942232755 0.222837253738 -0.0367191902643 0.272031025847 36.5488536012 -22.5772851803 -22.0030780105 11 7.35520422228 6.21300821737 -0.146999425317 8.58177333109 1.55624246611 2.1342027862 -0.0126204395589 -0.340988574555 0.809597215963 -0.277869450832 -0.0939142128772 0.922980726688 -0.388258008307 -0.320535933356 0.11817924569 0.377493745368 0.104067494384 -0.026803525925 0.43139702332 0.0239081378574 0.429695720762 23.1214624742 -21.0287786309 -23.5358190186 12 4.26111109314 3.62786716611 -4.33634321359 3.35112361389 -3.43776449718 6.17991580667 0.0836782794573 0.395428500955 0.733143589786 0.729567438358 1.04208621818 0.237932993889 -0.846871506441 -0.248492643593 -0.890879925201 0.473004736367 0.11313691884 -0.0519363105685 0.360627489117 -0.14081963052 0.584187252973 36.652645762 -6.14188560469 -25.3652206877 13 3.67000494987 -4.93626471611 -0.272995728055 9.45624323292 -3.94938349917 8.12021756224 -0.0989101140203 -0.95076368886 -0.523591616741 0.22907811026 0.500217921556 1.51007957867 -0.116091072463 -0.645062719797 -0.409844689802 0.305350473028 0.00305354715936 0.0067783101368 0.481827185729 -0.00663096224983 0.556345174046 16.1860262746 -43.102250051 -11.6786319977 14 7.75645873823 -3.30276034991 1.35551806848 7.7815163588 -5.76836109014 4.49184862726 -0.506936165776 -0.638287077808 -0.0854333129849 0.412492830147 -0.427897925584 0.0127550549815 -0.218475993266 -0.0655899420087 0.956186506664 0.452262812929 -0.0643161515825 -0.0764601029717 0.437102584992 -0.0397626121463 0.544954975083 24.4051851959 -44.3785525758 -3.49044821071 15 6.50993196861 5.22859729417 -0.934873324849 4.83544106435 0.964066749796 4.77808401392 0.701519872726 -1.00767661222 0.100353229712 0.770876090679 -0.656321800576 0.193552627697 0.573602609605 0.384612985947 -0.0369920463182 0.431282328503 0.0570468742399 -0.0324648864103 0.321279318737 0.0662421476172 0.363178902241 31.9447776073 -39.6313849251 -6.12192835759 16 7.3994303344 0.900908333684 1.0998117068 1.52444721094 -0.661610435959 1.89855409771 0.225028359546 -0.563587068324 -0.103815810741 0.195802914226 -0.16338428323 0.0859565056291 0.141785933622 -0.13984566895 -0.0496966622284 0.336788925521 0.0299952669466 -0.0071432701583 0.189267971558 -0.00767402595292 0.270965532359 35.9516526942 -30.1298873661 -11.4536576043 17 9.15379811434 2.48689433028 2.88425709357 4.26481578178 2.33612550364 2.58516494802 0.341051429082 0.141938972247 -1.32663748776 -0.355909711405 -0.0946514198993 -0.580914123096 0.306068415962 0.109812401129 -0.275275018111 0.444955838428 0.00368393540981 -0.0218024422131 0.21134566498 0.0555330644874 0.488009177378 36.5878519373 -40.3298525328 -15.7361880742
精密化 TLSグループ 大きな表を表示 (4 x 17) 大きな表を隠す ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 3 through 18 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 19 through 39 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 40 through 81 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 82 through 143 )5 X-RAY DIFFRACTION 5 chain 'B' and (resid 2 through 51 )6 X-RAY DIFFRACTION 6 chain 'B' and (resid 52 through 143 )7 X-RAY DIFFRACTION 7 chain 'C' and (resid 2 through 18 )8 X-RAY DIFFRACTION 8 chain 'C' and (resid 19 through 28 )9 X-RAY DIFFRACTION 9 chain 'C' and (resid 29 through 64 )10 X-RAY DIFFRACTION 10 chain 'C' and (resid 65 through 112 )11 X-RAY DIFFRACTION 11 chain 'C' and (resid 113 through 136 )12 X-RAY DIFFRACTION 12 chain 'C' and (resid 137 through 145 )13 X-RAY DIFFRACTION 13 chain 'D' and (resid 3 through 18 )14 X-RAY DIFFRACTION 14 chain 'D' and (resid 19 through 30 )15 X-RAY DIFFRACTION 15 chain 'D' and (resid 31 through 51 )16 X-RAY DIFFRACTION 16 chain 'D'