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- PDB-7ben: Crystal structure of the receptor binding domain of SARS-CoV-2 Sp... -

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基本情報

登録情報
データベース: PDB / ID: 7ben
タイトルCrystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253 and COVOX-75 Fabs
要素
  • COVOX-253 heavy chain
  • COVOX-253 light chain
  • COVOX-75 heavy chain
  • COVOX-75 light chain
  • Spike glycoprotein
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / antibody / germline / V-gene / receptor-binding-domain / spike / neutralisation / protection / glycosylation / valency / VIRAL PROTEIN / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
BROMIDE ION / IMIDAZOLE / IODIDE ION / DI(HYDROXYETHYL)ETHER / Chem-PG6 / Spike glycoprotein
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.5 Å
データ登録者Zhou, D. / Zhao, Y. / Ren, J. / Stuart, D.
資金援助 英国, 中国, 2件
組織認可番号国
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 英国
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 中国
引用ジャーナル: Cell / 年: 2021
タイトル: The antigenic anatomy of SARS-CoV-2 receptor binding domain.
著者: Wanwisa Dejnirattisai / Daming Zhou / Helen M Ginn / Helen M E Duyvesteyn / Piyada Supasa / James Brett Case / Yuguang Zhao / Thomas S Walter / Alexander J Mentzer / Chang Liu / Beibei Wang / ...著者: Wanwisa Dejnirattisai / Daming Zhou / Helen M Ginn / Helen M E Duyvesteyn / Piyada Supasa / James Brett Case / Yuguang Zhao / Thomas S Walter / Alexander J Mentzer / Chang Liu / Beibei Wang / Guido C Paesen / Jose Slon-Campos / César López-Camacho / Natasha M Kafai / Adam L Bailey / Rita E Chen / Baoling Ying / Craig Thompson / Jai Bolton / Alex Fyfe / Sunetra Gupta / Tiong Kit Tan / Javier Gilbert-Jaramillo / William James / Michael Knight / Miles W Carroll / Donal Skelly / Christina Dold / Yanchun Peng / Robert Levin / Tao Dong / Andrew J Pollard / Julian C Knight / Paul Klenerman / Nigel Temperton / David R Hall / Mark A Williams / Neil G Paterson / Felicity K R Bertram / C Alistair Siebert / Daniel K Clare / Andrew Howe / Julika Radecke / Yun Song / Alain R Townsend / Kuan-Ying A Huang / Elizabeth E Fry / Juthathip Mongkolsapaya / Michael S Diamond / Jingshan Ren / David I Stuart / Gavin R Screaton /
要旨: Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and ...Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC < 0.1 μg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.
履歴
登録2020年12月24日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年3月3日Provider: repository / タイプ: Initial release
改定 1.12021年4月7日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.22021年4月28日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.page_first
改定 1.32023年11月29日Group: Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name
改定 1.42024年1月31日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model
改定 1.52024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
E: Spike glycoprotein
H: COVOX-253 heavy chain
L: COVOX-253 light chain
A: COVOX-75 heavy chain
B: COVOX-75 light chain
C: Spike glycoprotein
D: COVOX-253 heavy chain
F: COVOX-253 light chain
G: COVOX-75 heavy chain
I: COVOX-75 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)241,56040
ポリマ－237,69110
非ポリマー3,86830
水4,197233
1
E: Spike glycoprotein
H: COVOX-253 heavy chain
L: COVOX-253 light chain
A: COVOX-75 heavy chain
B: COVOX-75 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)120,66819
ポリマ－118,8465
非ポリマー1,82314
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Spike glycoprotein
D: COVOX-253 heavy chain
F: COVOX-253 light chain
G: COVOX-75 heavy chain
I: COVOX-75 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)120,89121
ポリマ－118,8465
非ポリマー2,04616
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)93.188, 149.794, 229.099
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 1 through 142 or resid 149 through 192 or resid 194 through 228))
d_2ens_1(chain "G" and (resid 1 through 142 or resid 149 through 192 or resid 194 through 228))
d_1ens_2(chain "B" and (resid 1 through 2 or resid 5...
d_2ens_2(chain "F" and (resid 1 through 2 or resid 5...
d_3ens_2(chain "I" and (resid 1 through 2 or resid 5...
d_1ens_3(chain "C" and (resid 337 through 355 or resid 357 through 384 or resid 390 through 516))
d_2ens_3(chain "E" and (resid 337 through 355 or resid 357 through 384 or resid 390 through 516))
d_1ens_4(chain "D" and (resid 1 through 188 or resid 190...
d_2ens_4(chain "H" and (resid 1 through 188 or resid 190...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNSERK1 - 142
d_12ens_1THRLEUK145 - 188
d_13ens_1SERLYSK192 - 226
d_21ens_1GLNSERY1 - 142
d_22ens_1THRLEUY145 - 188
d_23ens_1SERLYSY190 - 224
d_11ens_2ASPILEL1 - 2
d_12ens_2THRPROL5 - 8
d_13ens_2SERSERL12
d_14ens_2SERSERL14
d_15ens_2GLYGLYL16
d_16ens_2THRTHRL20
d_17ens_2CYSGLNL23 - 27
d_18ens_2SERSERL31
d_19ens_2LEUGLYL33 - 41
d_110ens_2ALAPROL43 - 44
d_111ens_2LEUTYRL46 - 49
d_112ens_2SERSERL52 - 53
d_113ens_2GLYGLYL57
d_114ens_2PROPROL59
d_115ens_2ARGSERL61 - 76
d_116ens_2LEULEUL78
d_117ens_2PROALAL80 - 84
d_118ens_2TYRGLNL86 - 90
d_119ens_2SERSERL93
d_120ens_2PROPROL95
d_121ens_2THRGLYL97 - 99
d_122ens_2GLYLEUL101 - 125
d_123ens_2SERSERL127 - 162
d_124ens_2THRALAL166 - 195
d_125ens_2GLUGLUL197 - 215
d_21ens_2ASPILEU1 - 2
d_22ens_2THRPROU5 - 8
d_23ens_2SERSERU12
d_24ens_2SERSERU14
d_25ens_2GLYGLYU16
d_26ens_2THRTHRU20
d_27ens_2CYSGLNU23 - 27
d_28ens_2SERSERU31
d_29ens_2LEUGLYU34 - 42
d_210ens_2ALAPROU44 - 45
d_211ens_2LEUTYRU47 - 50
d_212ens_2SERSERU53 - 54
d_213ens_2GLYGLYU58
d_214ens_2PROPROU60
d_215ens_2ARGSERU62 - 77
d_216ens_2LEULEUU79
d_217ens_2PROALAU81 - 85
d_218ens_2TYRGLNU87 - 91
d_219ens_2SERSERU94
d_220ens_2PROPROU96
d_221ens_2THRGLYU98 - 100
d_222ens_2GLYLEUU102 - 126
d_223ens_2SERSERU128 - 163
d_224ens_2THRALAU167 - 196
d_225ens_2GLUGLUU200 - 218
d_31ens_2ASPILEI1 - 2
d_32ens_2THRPROI5 - 8
d_33ens_2SERSERI12
d_34ens_2SERSERI14
d_35ens_2GLYGLYI16
d_36ens_2THRTHRI20
d_37ens_2CYSGLNI23 - 27
d_38ens_2SERSERI31
d_39ens_2LEUGLYI33 - 41
d_310ens_2ALAPROI43 - 44
d_311ens_2LEUTYRI46 - 49
d_312ens_2SERSERI52 - 53
d_313ens_2GLYGLYI57
d_314ens_2PROPROI59
d_315ens_2ARGSERI61 - 76
d_316ens_2LEULEUI78
d_317ens_2PROALAI80 - 84
d_318ens_2TYRGLNI86 - 90
d_319ens_2SERSERI93
d_320ens_2PROPROI95
d_321ens_2THRGLYI97 - 99
d_322ens_2GLYLEUI101 - 125
d_323ens_2SERSERI127 - 162
d_324ens_2THRALAI166 - 195
d_325ens_2GLUGLUI197 - 215
d_11ens_3PROARGP2 - 20
d_12ens_3ARGPROP22 - 49
d_13ens_3LEUGLUP52 - 178
d_21ens_3PROARGA1 - 19
d_22ens_3ARGPROA21 - 48
d_23ens_3LEUGLUA51 - 177
d_11ens_4GLNLEUQ1 - 183
d_12ens_4SERHISQ187 - 207
d_13ens_4PROLYSQ209 - 221
d_14ens_4FUCFUCR
d_15ens_4NAGNAGS
d_16ens_4NAGNAGT
d_21ens_4GLNLEUE1 - 183
d_22ens_4SERHISE185 - 205
d_23ens_4PROLYSE207 - 219
d_24ens_4FUCFUCF
d_25ens_4NAGNAGG
d_26ens_4NAGNAGH

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixベクター
1given(0.999974832216, -0.00285034136601, 0.0064969600227), (-0.00287526189799, -0.999988533395, 0.00382961441311), (0.00648596981625, -0.0038481984918, -0.999971561378)51.4043468154, 75.339371489, -114.37831931
2given(-0.029310701686, 0.523552801294, 0.851488900118), (0.741632719915, 0.582519806778, -0.332643327699), (-0.670165495619, 0.621742019626, -0.405357952325)111.836641397, 17.2511559482, -102.478933336
3given(0.999992306292, 0.000746568050574, 0.00385097311061), (0.000721043858558, -0.99997779369, 0.00662512052478), (0.00385583369802, -0.00662229283252, -0.999970638461)51.0440336939, 75.6129709016, -114.425418794
4given(0.999996960242, -0.000226842298047, 0.0024552085303), (-0.000240230205844, -0.999985098308, 0.0054539391357), (0.00245393475945, -0.00545451237229, -0.99998211309)-50.7011421035, 75.0688944166, -114.323598823
5given(0.999991866953, 0.00275935977638, 0.00294142168108), (0.0027494669982, -0.999990568586, 0.0033620188224), (0.00295067095882, -0.0033539041371, -0.999990022384)-50.8219093681, 74.7964905876, -114.411556615

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要素

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抗体 , 4種, 8分子 HDLFAGBI

#2: 抗体 COVOX-253 heavy chain


分子量: 24371.400 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 COVOX-253 light chain


分子量: 23256.641 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#4: 抗体 COVOX-75 heavy chain


分子量: 24821.846 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#5: 抗体 COVOX-75 light chain


分子量: 23244.861 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

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タンパク質 / 糖 , 2種, 4分子 EC

#1: タンパク質 Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


分子量: 23150.891 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2
#6: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 570.542 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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非ポリマー , 7種, 261分子

#7: 化合物
ChemComp-IMD / IMIDAZOLE


分子量: 69.085 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C3H5N2
#8: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C3H8O3
#9: 化合物
ChemComp-BR / BROMIDE ION


分子量: 79.904 Da / 分子数: 14 / 由来タイプ: 合成 / 式: Br
#10: 化合物 ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


分子量: 266.331 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C12H26O6
#11: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER


分子量: 106.120 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C4H10O3
#12: 化合物 ChemComp-IOD / IODIDE ION


分子量: 126.904 Da / 分子数: 1 / 由来タイプ: 合成 / 式: I
#13: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 233 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.36 Å3/Da / 溶媒含有率: 63.43 % / 解説: presence of translational NCS
結晶化温度: 294 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5 / 詳細: 0.1 M BIS-TRIS pH 6.5, 16% (w/v) PEG 10000

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I03 / 波長: 0.97625 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2020年11月20日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97625 Å / 相対比: 1
反射解像度: 2.5→59.1 Å / Num. obs: 111578 / % possible obs: 100 % / 冗長度: 26.6 % / Biso Wilson estimate: 62.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.283 / Rpim(I) all: 0.056 / Net I/σ(I): 7.3
反射 シェル解像度: 2.5→2.54 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 5490 / CC1/2: 0.623

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解析

ソフトウェア
名称バージョン分類
GDA1.18.1_3865データ収集
PHENIX1.18.1_3865精密化
xia2データ削減
xia2データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7BEL

7bel


解像度: 2.5→58.38 Å / SU ML: 0.5113 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 37.0862
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2822 5570 5.03 %
Rwork0.2404 105179 -
obs0.2425 110749 99.31 %
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: 72.1 Å2
精密化ステップサイクル: LAST / 解像度: 2.5→58.38 Å
タンパク質核酸リガンド溶媒全体
原子数16008 0 191 233 16432
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002516593
X-RAY DIFFRACTIONf_angle_d0.584322558
X-RAY DIFFRACTIONf_chiral_restr0.04452530
X-RAY DIFFRACTIONf_plane_restr0.00432891
X-RAY DIFFRACTIONf_dihedral_angle_d18.90795944
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2GX-RAY DIFFRACTIONTorsion NCS0.413123418084
ens_2d_2FX-RAY DIFFRACTIONTorsion NCS1.46263126394
ens_2d_3IX-RAY DIFFRACTIONTorsion NCS0.450582424414
ens_3d_2EX-RAY DIFFRACTIONTorsion NCS0.498731907466
ens_4d_2HX-RAY DIFFRACTIONTorsion NCS0.500308342907
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.49581720.47153167X-RAY DIFFRACTION90.22
2.53-2.560.49921620.44393399X-RAY DIFFRACTION97.43
2.56-2.590.43231690.42743506X-RAY DIFFRACTION99.54
2.59-2.620.42331840.39853443X-RAY DIFFRACTION99.81
2.62-2.660.45421930.38773514X-RAY DIFFRACTION99.81
2.66-2.690.40581870.3453435X-RAY DIFFRACTION99.61
2.69-2.730.36221800.3383532X-RAY DIFFRACTION99.7
2.73-2.770.39751700.33723460X-RAY DIFFRACTION99.62
2.77-2.820.37151900.31953497X-RAY DIFFRACTION99.7
2.82-2.860.3511780.31783468X-RAY DIFFRACTION99.81
2.86-2.910.40062030.32083498X-RAY DIFFRACTION99.81
2.91-2.960.38991760.31563467X-RAY DIFFRACTION99.73
2.96-3.020.32531940.30393516X-RAY DIFFRACTION99.92
3.02-3.080.38152030.30283468X-RAY DIFFRACTION99.73
3.08-3.150.36852020.30023490X-RAY DIFFRACTION99.86
3.15-3.220.3491780.27453529X-RAY DIFFRACTION99.87
3.22-3.30.29761690.25553496X-RAY DIFFRACTION99.86
3.3-3.390.26211970.24643516X-RAY DIFFRACTION99.87
3.39-3.490.28481970.23973497X-RAY DIFFRACTION99.89
3.49-3.610.28812030.24053529X-RAY DIFFRACTION99.92
3.61-3.730.27711740.23173537X-RAY DIFFRACTION99.87
3.73-3.880.26571760.22513535X-RAY DIFFRACTION99.84
3.88-4.060.23331960.20643504X-RAY DIFFRACTION99.84
4.06-4.270.21161810.18933553X-RAY DIFFRACTION100
4.27-4.540.21221880.17323552X-RAY DIFFRACTION99.95
4.54-4.890.20751810.1753590X-RAY DIFFRACTION99.95
4.89-5.380.21131950.18153547X-RAY DIFFRACTION99.84
5.38-6.160.27762000.20493602X-RAY DIFFRACTION99.95
6.16-7.760.25091930.22883636X-RAY DIFFRACTION99.9
7.76-58.380.26951790.21843696X-RAY DIFFRACTION96.85
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
15.138876857574.49903499991.01182954125.042119844350.2346965787350.636972913535-0.2932036875561.55049958690.269661568734-1.27214531551-0.449467337761-1.661840826970.7323179760890.736184497820.7010538695580.798736968050.01147492084460.07694249103340.8130810660910.1775720239661.1519520958814.747962288633.6651104425-89.5820372209
20.8065248358710.1656094423290.7355900247437.01032859402-2.582252891543.551177816630.316139463477-0.07897549221770.4509898237650.304975791321-1.06921669175-1.35725396581-0.5123865517741.285404503620.6069987982250.875840594034-0.145935335517-0.1344598087590.7697584260480.07448189952331.1284038099719.014355211347.8299910647-88.2305982614
32.152608850082.63807727748-1.660741123959.28235544329-0.9936699493138.683885650080.0353171748323-0.5439834145870.3109656013490.82290922294-0.5699253933960.86463823948-0.682753204024-0.2737618117060.4936587042930.633992492209-0.0651065626561-0.1545979830550.608373267968-0.2095442696560.6068089075967.2617845684739.4010830429-79.8586950707
44.303971587644.996189243870.6166210531848.46675560118-0.4400270171142.612363294370.115104438953-0.4130101814050.1214426853320.280222803306-0.759746304146-0.0439615860597-0.3562956583330.3146340952330.6423544003710.40381524346-0.0164432026787-0.06065743025550.461680948711-0.08164784883990.6412085660037.5792284215533.9975411157-81.1636203926
51.862254949861.15547691942-3.024681268390.966271101983-2.078418903865.01114720830.102496887816-0.0131531915502-0.384670777929-0.3193120352610.3966638281120.4315947628640.1262699505610.0897627614724-0.5940441726350.705195763572-0.216629433245-0.03453494168980.545973802526-0.0570336526730.731554626913-1.2020269425119.2403698241-69.6009257161
66.764004314714.160794311286.224514960767.109759542924.065078298468.12544782078-1.014949184650.5939525402472.81239653445-0.151980423996-0.4959022188821.48759243789-0.573214195561-0.1390067456381.053003420520.6520835563350.0447247893899-0.1515763666510.520755148662-0.1342070059680.8014720659964.4026901926137.1958470394-88.6144625815
75.60532487934-1.22390113666-0.6389626820753.80681002316-0.9413095310385.36441850094-0.02078090385640.03138669211240.301901949997-0.08391720964960.133154474648-0.0819081998661-0.115878976358-0.169136192989-0.04061090373210.620473897967-0.189615106351-0.03314283882930.4919264709170.008519423499020.451207059601-22.618220737123.0575699086-74.229146449
86.205089297170.790338609002-0.77896390660.773755337833-0.3350880372170.95180458632-0.1894182351730.8690598867830.784795167693-0.1481389539490.04950325306820.0833257621133-0.151967106076-0.0285702800740.2064783402120.752432998667-0.158095433893-0.05016313922470.499983779610.0315763284210.615239475997-29.148114745223.8303384509-73.5639572512
94.54055950130.740315784619-1.629569222672.186178883260.3444955811887.20791358944-0.0312408324071-0.07580053441090.91375231348-0.139267505657-0.05209492702850.571965192259-0.4821851096150.21017055287-0.008372506491820.5769173218920.0114914190926-0.06017249886460.5853614331710.01496375371940.660635078991-55.097748840825.996150666-64.4592328735
103.46481555373-1.39152915888-3.874853198684.459596745450.8382720426624.28319894869-0.52656091385-0.6621237350940.03024433524670.1750868391250.82465151013-0.001621688663181.081443086140.219160814217-0.05606266445620.635904899261-0.0486155405109-0.1047799847870.8025014169050.04917252867390.512951492406-28.04963261945.8140084429-55.8551489885
112.501057047992.236844267610.05860365157322.91237760508-1.622745114412.670685087530.175690325988-0.284387108576-0.2466397341770.15048552876-0.140432704370.1631816685630.111773901412-0.0730607864427-0.04236627138240.482559388498-0.135765041262-0.03167198062450.55540292644-0.05958911986270.356888473856-21.246055448712.3863693738-58.9654570869
124.99692403809-0.993930365142-0.05421143360133.41528072154-0.8356794309524.449636779960.024208115987-1.115453767650.6705439958870.993087677060.139688716099-1.084947533490.1324858213950.1273235607670.04294403913960.820242551625-0.143814296784-0.0398008111920.7088287709520.02968626028620.43327373578-17.868719810112.8703418693-51.5762276902
136.829713134261.020178185850.598066332380.4742413307450.02586758270870.268867648627-0.104639920482-0.3669151531120.1888706123310.013918077325-0.003611077378650.0463820381466-0.0976448247882-0.3017637416290.1568819117310.556606611677-0.03273468947190.0187863047010.585125359408-0.03749447121150.423953141323-44.191882895711.8725048989-60.248453162
146.117608788215.200000736232.453719873214.406788130562.461597938616.12289779358-0.3780305690420.992054120222-1.287707359140.07781484888451.02407300467-0.87641020661-0.0489684585132-0.301451042774-0.7306691086910.5644459945860.00811034977521-0.01429877054720.780142727672-0.01462000653360.73370987466-57.33205874635.5227373593-70.2408466735
157.345610063460.2067038305112.098445649122.69856096625-0.9284226545713.166892472590.0351074724822-0.198515100290.01700523124430.1177299449120.1155507647220.437584387084-0.109355135806-0.112408986106-0.04915492339660.505886220617-0.05258139913150.01805999615080.658714572296-0.05750005362250.53166582501-59.76317376389.15530492395-63.1829329647
162.860956248311.50691627633-1.275195786991.028799549430.5469884542336.24669981245-0.0240707326511-0.0770156693113-0.01879270850180.0307377181971-0.3144073060490.2277946382510.350235239572-0.359746070399-0.01138534992650.4942128589120.0240585137114-0.008105197530180.599800593649-0.1471078258130.750103455306-19.65193987767.90881708538-112.072146519
174.94428953274-0.1680662968491.440245213573.8320147941-0.5527436192586.39955337874-0.151532848343-0.2563471623050.4659189050920.142897364977-0.03363594911390.420105223388-0.32436515438-0.4184601229030.09402425823730.3889218111470.02665953254020.01162412744650.429862459097-0.1334688629030.456352013151-13.565381144515.6445435228-104.559111867
182.76771674410.5578006077962.241902242741.610254902612.019362435494.95123813009-0.0222027276925-0.1278515639210.303830826960.00297597963457-0.187244660.120685021036-0.178564091004-0.2287553297090.1050117975220.4131837753360.0310553332854-0.01282770394030.414568868527-0.05136981788150.484223266125-13.682502899314.8242612394-104.344938626
190.893626303103-0.756192030272-2.112226157395.545753874523.323431544916.03688691351-0.2028101580910.4739183309940.00886041084017-0.4691878426270.28425928926-0.7484258178550.167601721150.01447851984120.09163262880940.49761631255-0.03589551863330.06398231677490.622798492193-0.1682030563390.429528069379-9.80745731624-5.5159504102-135.618261604
205.30117571922-0.879497935975-0.310418102944.370020431981.572097509822.18271683536-0.0543318188508-0.0859284795496-0.2353710329870.1152538639170.135665889079-0.5166630856920.1223034348470.340376253496-0.08930081755470.4121386484990.0372235820666-0.01446015663480.573883222512-0.05434817597870.432106100406-8.50816186862-6.56423795374-129.529214971
216.63837476891-2.405836982560.2324811054255.73431225364-1.976345711753.245753147810.3997324997260.286771699043-0.798163881752-0.480478170348-0.46711678241-0.6686512760180.8014905980620.233211499013-0.05728094881280.6070016505860.0743226992129-0.04187395114040.504680805832-0.05120220907880.478352479286-7.40818173541-14.1086131864-131.604220254
221.48597860178-1.717671241491.394739474615.78769564898-1.699568708861.265567764530.4898088945360.0808206870342-0.0257101575087-0.940857626411-0.117700202437-0.17378409209-0.542653735880.132311081456-0.3959986721370.496205976909-0.09030512413820.006861741265570.437489925413-0.1980186974860.531785901901-13.9522712766-15.3236064305-135.439105604
232.4376532529-1.14858116936-3.108063683738.139210452152.028106954573.723383868920.3109033871320.08101548742710.284781486567-0.309588545601-0.255657586378-0.6533240843430.007547294416270.943016371953-0.1505348001910.373597567564-0.0778765755579-0.03296431369710.92372406074-0.02281558128370.5337818548511.57935976819.92895835337-110.939131174
245.31934920489-1.245705084730.1243946136664.967563610052.474810328144.57082763814-0.0395768752554-0.431799672680.3608251957270.04837568449760.436692491191-0.805637877095-0.01278580910921.16831780593-0.4838401236530.3959462006650.0105134878442-0.0435653545210.708048998297-0.1022221977280.4961604468266.6691720916911.4145581663-102.129776379
256.35165334349-2.89066265370.02380184594046.854801729571.36692615664.8327955308-0.02984433159490.293149991907-0.566121766241.16851323363-0.1493897774860.279982392160.6136627861340.806735554655-0.4876615240790.5598417949280.14569730724-0.1638494149070.732575764479-0.1999515867010.55823499997.316583595353.89516623192-106.486998001
264.43881890178-1.31846450970.1892248369334.040300097852.045646346643.261013497080.2457168474370.3084128716981.06404587136-0.5877085253520.475007230197-0.129235523831-0.4219638230060.19183999068-0.2607347741240.520153313622-0.168184552609-0.02465805911060.4271106149480.1897043045150.438858230857-0.31840711549719.3953120885-107.383052725
271.64891015308-1.90522709335-3.292159270525.151829115065.446288079147.507457493280.3081060731671.284787523840.3202171989130.4488514350520.352939426181-0.9953067519010.471739384571-0.178942871145-0.6848718835720.5175318332740.273754857018-0.1192545321730.795532135525-0.1278438289590.77144550863714.1204617553-3.98700231094-120.26572565
289.05102392528-1.935687855522.068316341475.359547405560.7998150038323.13374535852-0.140024920057-0.429729483954-0.205921178965-0.2532881271550.264791232105-0.255891172021-0.207266847122-0.215371648232-0.04774419290950.387475469049-0.02571365823460.07515732977420.668556478381-0.07940709229790.4433907107181.89248828618-3.93971171064-138.348843549
293.323868055850.6593354896444.677011838335.30210604587-0.9460865294037.11499075351-0.394804035337-0.06813588170590.284857459201-0.7561712042110.0571455153839-0.132429088187-0.7052461605860.3800800372570.2159686738470.593938753551-0.060828210480.1072368817380.642851107531-0.0393424050780.7351994170622.996679929954.6785049778-140.400318207
305.8709995716-1.012896116851.334594729211.53373948177-0.251761566164.19815383237-0.07783353206370.8602415827420.0102869842026-0.1183720768260.0880036611181-0.113700742379-0.07308429589580.939019547139-0.06665371152860.4604932194960.01148356445550.02561311549050.763242649768-0.1775286079920.5331207753164.99131995385-3.30698954624-139.319288798
316.74956556906-6.10067750943.519605595416.85317918061-5.148417746296.578829966940.223409169939-0.8367737901010.1676500617290.233244835021-0.357947918287-1.882168359570.558480937150.6320421843480.2223172713510.7948524064080.055573076022-0.2359639959470.8431349438430.146672579291.3062713126869.964818372837.7808991911-25.5360122268
323.38295038397-2.91172842708-2.475166587045.54894889841.427792101958.432647481430.0671223187130.04029959901790.3708505651330.08911915927330.2542463689280.214751751403-0.271185409766-0.368672445123-0.4225345155640.7641327032040.07089342463480.05465256100940.467159057046-0.01036128752641.0245738330262.293194732325.0419997878-23.0460711029
332.22346031942-2.2625608077-0.3774456482337.508789482561.882535005574.244743791580.1725091259020.552435417982-0.558421361916-0.337774880005-0.796419680505-0.1114943530260.485940950319-0.1011012856570.5730620563670.4984869585210.07964915472360.07536070184220.571313481262-0.01449724707970.71168212911859.781618141937.2339862068-33.3732371622
343.07657106955-1.488110015720.02091540494411.51983001678-0.656364483723.10437909658-0.116549273683-0.06318243006210.113630145559-0.023261642149-0.3507966363570.0756302902496-0.0815790328108-0.3931275309620.5489647545050.5687206989920.00497341192984-0.04069520429240.531757806881-0.1827103922750.78511887155752.268571121547.0051809638-35.7126157873
354.34594562517-3.21655239913-5.793271305093.673081485584.141762262967.88380478289-0.643220857408-1.24889173453-0.7201983324720.4426576563180.685868516722-0.3365665432611.620073585970.968790645120.0236008901880.9407501185670.175068709056-0.1058164484880.6294506605010.08889175776660.76568614624520.852196514646.1188985673-38.3817903562
363.956568586220.7150229988030.8831785918432.23608507665-1.525891160992.59684574977-0.1350003062250.206305500366-0.519684620490.231411252724-0.151177011748-0.4183219268840.108981834956-0.1378718763380.2131021126940.6431100291260.122395863598-0.09677706842950.588182202965-0.003148968951950.56572407654329.229672354352.3031615475-42.6327695629
374.22849849297-3.82696649055-1.833618989023.993585937470.6248881368467.45108734794-1.39986585714-0.2186212337171.481267570392.547429681681.13274479906-0.834947609005-0.6539621044310.1551835123690.2819270671650.9184084212820.0736801502534-0.09281971123060.5573787725630.016732385370.76073530634535.201217965357.7876309458-35.52788341
388.91011453038-5.91146132981-3.883475983453.812647290232.287627514958.77138204250.409674354606-1.60078075271-1.05958053212-0.845218661955-0.0760309554474-0.136235282903-0.1287224087090.089733600329-0.2783078239570.7405834325050.137215071646-0.1131113418830.7925519630230.07566195541840.67081056207531.428379691249.0937581263-34.0099593847
397.97043786987-1.76257357577-5.209402698032.99623057120.4964625964839.365613723120.497539520475-1.314296857220.4558208625630.1133427484940.506093862964-0.279535054023-0.7481540062890.398212693154-0.8594089748940.5569940753450.0876700320066-0.09448382654710.7548873339990.1021434941350.60383730421320.54281556455.6288903849-36.7058925159
404.07039587661-1.25974292224-0.779913410091.58230964620.00347266807692-0.0492705057550.235104474184-0.0712380473518-0.48758344030.0906995312127-0.1118342770490.2699234407830.006526657072010.0102127815106-0.1841747757760.7211006813250.118906815838-0.004323062490810.685244814966-0.0575196339410.55922863254716.945407725149.9754721987-46.1978350216
419.29478413009-1.61480847492.311390452314.463573758830.7230226295917.288080269180.0886912981946-0.912349098569-0.94336250698-0.271783130688-0.1558113990930.2850086555971.14041256231-0.4532661378840.3745015260740.663104810317-0.0807239984717-0.0200090502880.4942702676580.0871448995330.94920819088-2.543547985948.8777119851-48.4354849934
424.413053038890.479257255324-0.1848141416984.380717453191.812286101854.00554699532-0.1187398931350.336617434744-1.11963345442-0.06509127443330.04211038979970.4411448539820.495089450305-0.2967437083480.03578602250470.6397392795350.028984345092-0.07072874749070.566906120545-0.1129398599190.859485359966-5.1734910755248.5590591651-50.82593027
434.591026241692.804899180694.551665391244.8632982130.8104683124095.423269727980.03068888316170.1002366228930.638451081394-0.529795644086-0.224737453959-0.174786070837-0.341151408116-0.3198205343140.3581721838290.6106949629050.121569535670.03689840503430.698857935892-0.1196493595150.54688666013526.716877366769.7773195902-57.3064053922
443.085742745570.703570315219-0.05514046402943.65134466663-0.7496134556464.047190462740.1494627355610.793312990721-0.381084415268-0.6846151158360.00640877797492-0.360635225240.4721545808490.252169512021-0.08242444433640.6144755230120.211596500237-0.06056093170660.697621312666-0.1233286885610.49538707492530.688892289259.8530779397-59.6715148756
455.324548002210.47344204769-0.01147551031151.39862617344-1.51271232561.35963753468-0.08437808443620.651857480465-0.442742326249-0.2832637767540.06296727847640.09037964883570.218336617916-0.1710294633460.07974302448610.6699205612180.133311798319-0.1521032863730.663007886512-0.1877864037320.48402636729321.150327500463.0559790009-58.5842418447
468.7432441349-0.928176992543-1.213977648374.29614361158-1.179047233593.66340082427-0.0675343944662-0.32347962079-0.289755024741-0.009873121616290.1685232693850.4774545011850.115469130791-0.496534406813-0.1040430660870.5960864862620.0136242106175-0.1151623033480.7365845860730.07103872311820.579400727789-7.7978235325464.1466379456-48.6068360218
476.17871746770.429005252885-2.137196843411.06810721754-0.3764758645932.142765779510.1585426960930.237646948672-0.0964694332725-0.1859524806420.1268015871970.3695436255460.0297246364685-0.0974207191211-0.3729072919720.5694187013250.0787108410977-0.1528886701050.774074087299-0.01628591585930.651041237542-9.0846337916965.4241019544-51.4138232545
483.83059913106-0.90423780406-1.57489062772.240235875261.936013574982.5282826561-0.1329294937990.447441788262-0.287020997803-0.233078253931-0.3793117909530.377920207462-0.462456629933-0.5608191381060.4970363723510.481983068354-0.0222496476431-0.07971049213190.471166886109-0.01200110362580.55211678175531.957284188665.6713786228-9.37267919593
492.690335258660.276649512317-2.34769710930.9152448348791.314287875565.44282219369-0.1999987697310.0485630595352-0.1715731644040.045143209628-0.05109670430910.1997697137740.573403640299-0.05345811398130.1934910682720.469550166906-0.0207394570183-0.01084783484810.380471588217-0.0423413175630.59154339267237.770662869859.0049976031-9.10564166815
502.06776663880.698269432156-0.4838962296445.515567247040.681511458322.51864604073-0.0299122501404-0.3657365688210.2654918069710.2409023805680.095595408244-0.0433604470381-0.112310312260.254340104699-0.1211700101040.3420789894460.001327709813360.02405486053620.477681593331-0.01552963894370.41730850587741.629459832581.063359888417.1485662844
517.965654206155.234591993160.7321062192557.36304849851-0.5896722662974.599069123920.17150432743-0.6094750358080.2255572795480.856023739913-0.393493401746-0.73296109652-0.9702093917870.2130606346510.1922490728010.641231622286-0.0503438627148-0.08131904502220.397362227554-0.03660311956050.62279743091443.101157530789.16506007917.2331325991
524.42184999393.08790624643-1.737080588727.72127414588-2.369179582793.911363968281.33615485502-1.14098002965-0.1558486886180.983544840901-0.676611475061-0.6046675670060.81230880415-0.0799625671814-0.2105582924420.5523506457020.121196368978-0.02884969510180.397513476552-0.09005633854030.44693667527936.67264509690.190855516221.1700447176
533.498931711872.776763531711.755349551643.141584917343.325628703124.684533728060.260946595264-0.295209762133-0.3453016011890.2856872692550.226547134371-0.6205043380820.2888865206911.33169912241-0.4825230159330.607664102890.04973079210230.01997817184980.881502825945-0.2684917062130.83376414894662.086461270564.7982822051-3.3077238695
545.006582872561.27508301464-0.04435246295438.259843303713.436078997027.325628134730.008451518824660.39481145298-0.228897230546-0.490561358710.595667854639-0.888016182879-0.009353658280141.30801616101-0.6067518756010.463399086205-0.03397196615440.0452967196950.714741155795-0.1562104701580.50132329147457.346235584463.5186379965-12.295723637
555.014329430045.01724032205-0.2606993412475.13977533061-1.080951867336.787224372890.406807916441-0.5896747224560.0701873958651-0.525106026696-0.3672027614550.0275760370994-0.70112070651.50240551638-0.06750927011550.563919248522-0.06453288583780.08359681386030.770564811246-0.1260442023050.67011208996358.01062010371.0333087273-7.94902848426
562.85792682573-1.18144646233-0.6127198778321.801462923611.804712024014.56784474878-0.0653990039090.0098911237274-0.074489830649-0.08359846058160.1392302176010.1464179095510.02609147103160.672841421861-0.1998510689980.4249438971720.0657018663694-0.02108739897480.4760354767690.004613417340170.48606578187857.311300452766.9385750677-0.77401923121
572.043447557583.67413162735-2.49139562354.80963913491-2.904821629624.336066657640.202762089894-0.5504283181022.343234981690.3555988123580.792733647280.252716444575-0.108208839490.0791152439104-0.6075018445530.520285876235-0.035211717121-0.05203845844720.989132583693-0.1028600059970.45157386466345.645400469382.376829824529.0349423799
587.871674965421.72502288945-5.741236135684.903877133210.1157477898979.9722566206-0.0472657554862-0.366111980073-0.673996623981-0.1431658736390.186263184857-0.2931541787770.294034341180.979721886149-0.3250650627970.433979154506-0.0260904794646-0.1200772416510.653687235839-0.1550194024190.56240875840256.717492080676.226812466320.5292423382
595.95604113984-2.105615475861.894390948265.89734945882-4.482217180293.387226785540.020031403375-0.937983430139-0.3254222041040.6843398598030.898647567930.188525169075-0.304102618403-0.152816446205-0.5848403228410.5550484728590.07024545667760.009598390101790.660971841257-0.02890594910310.76726962000553.49096686970.023612013525.9039617575
606.048281555620.672254264941-3.364659345161.0034105725-0.5878004838126.48982952153-0.215517663433-0.505425468011-0.202175298870.314673960852-0.0277832881822-0.273461091931-0.0362730057834-0.0903997378620.1135183190560.515664392512-0.00681278744302-0.128619531520.681810862447-0.06675058924430.69288314561153.373028318477.047952331723.1653690117
619.510464670970.763277609555-4.778124422311.68954426798-1.645882447816.28593020275-0.170156509866-1.95794268088-0.6184655171150.533635030030.2249156984550.0571229909146-0.4382104956561.72003206641-0.04072105046320.6151236629120.0345909010996-0.1830285205611.23851768017-0.03939622961150.53935751807260.848752573880.222841476329.2797937401
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 337 through 353 )EA337 - 3531 - 17
22chain 'E' and (resid 354 through 393 )EA354 - 39318 - 54
33chain 'E' and (resid 394 through 421 )EA394 - 42155 - 82
44chain 'E' and (resid 422 through 469 )EA422 - 46983 - 130
55chain 'E' and (resid 470 through 494 )EA470 - 494131 - 155
66chain 'E' and (resid 495 through 516 )EA495 - 516156 - 177
77chain 'H' and (resid 1 through 64 )HE1 - 641 - 64
88chain 'H' and (resid 65 through 144 )HE65 - 14465 - 139
99chain 'H' and (resid 145 through 224 )HE145 - 224140 - 219
1010chain 'L' and (resid 1 through 18 )LI1 - 181 - 18
1111chain 'L' and (resid 19 through 49 )LI19 - 4919 - 49
1212chain 'L' and (resid 50 through 76 )LI50 - 7650 - 76
1313chain 'L' and (resid 77 through 151 )LI77 - 15177 - 151
1414chain 'L' and (resid 152 through 164 )LI152 - 164152 - 166
1515chain 'L' and (resid 165 through 214 )LI165 - 214167 - 218
1616chain 'A' and (resid 1 through 17 )AK1 - 171 - 17
1717chain 'A' and (resid 18 through 64 )AK18 - 6418 - 64
1818chain 'A' and (resid 65 through 123 )AK65 - 12365 - 123
1919chain 'A' and (resid 124 through 149 )AK124 - 149124 - 145
2020chain 'A' and (resid 150 through 189 )AK150 - 189146 - 185
2121chain 'A' and (resid 190 through 217 )AK190 - 217186 - 215
2222chain 'A' and (resid 218 through 228 )AK218 - 228216 - 226
2323chain 'B' and (resid 1 through 18 )BL1 - 181 - 18
2424chain 'B' and (resid 19 through 75 )BL19 - 7519 - 75
2525chain 'B' and (resid 76 through 90 )BL76 - 9076 - 90
2626chain 'B' and (resid 91 through 102 )BL91 - 10291 - 102
2727chain 'B' and (resid 103 through 113 )BL103 - 113103 - 113
2828chain 'B' and (resid 114 through 150 )BL114 - 150114 - 150
2929chain 'B' and (resid 151 through 163 )BL151 - 163151 - 165
3030chain 'B' and (resid 164 through 213 )BL164 - 213166 - 215
3131chain 'C' and (resid 336 through 365 )CP336 - 3651 - 30
3232chain 'C' and (resid 366 through 380 )CP366 - 38031 - 45
3333chain 'C' and (resid 381 through 469 )CP381 - 46946 - 131
3434chain 'C' and (resid 470 through 516 )CP470 - 516132 - 178
3535chain 'D' and (resid 1 through 17 )DQ1 - 171 - 17
3636chain 'D' and (resid 18 through 52 )DQ18 - 5218 - 52
3737chain 'D' and (resid 53 through 64 )DQ53 - 6453 - 64
3838chain 'D' and (resid 65 through 83 )DQ65 - 8365 - 83
3939chain 'D' and (resid 84 through 98 )DQ84 - 9884 - 98
4040chain 'D' and (resid 99 through 144 )DQ99 - 14499 - 139
4141chain 'D' and (resid 145 through 167 )DQ145 - 167140 - 162
4242chain 'D' and (resid 168 through 224 )DQ168 - 224163 - 221
4343chain 'F' and (resid 1 through 30 )FU1 - 301 - 30
4444chain 'F' and (resid 31 through 76 )FU31 - 7631 - 76
4545chain 'F' and (resid 77 through 114 )FU77 - 11477 - 114
4646chain 'F' and (resid 115 through 164 )FU115 - 164115 - 166
4747chain 'F' and (resid 165 through 214 )FU165 - 214167 - 218
4848chain 'G' and (resid 1 through 33 )GY1 - 331 - 33
4949chain 'G' and (resid 34 through 123 )GY34 - 12334 - 123
5050chain 'G' and (resid 124 through 189 )GY124 - 189124 - 185
5151chain 'G' and (resid 190 through 217 )GY190 - 217186 - 213
5252chain 'G' and (resid 218 through 228 )GY218 - 228214 - 224
5353chain 'I' and (resid 1 through 18 )II1 - 181 - 18
5454chain 'I' and (resid 19 through 75 )II19 - 7519 - 75
5555chain 'I' and (resid 76 through 90 )II76 - 9076 - 90
5656chain 'I' and (resid 91 through 113 )II91 - 11391 - 113
5757chain 'I' and (resid 114 through 128 )II114 - 128114 - 128
5858chain 'I' and (resid 129 through 150 )II129 - 150129 - 150
5959chain 'I' and (resid 151 through 163 )II151 - 163151 - 165
6060chain 'I' and (resid 164 through 198 )II164 - 198166 - 200
6161chain 'I' and (resid 199 through 213 )II199 - 213201 - 215

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る