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- PDB-7zfa: SARS-CoV-2 Omicron RBD in complex with Omi-6 and COVOX-150 Fabs -

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Basic information

Entry
Database: PDB / ID: 7zfa
TitleSARS-CoV-2 Omicron RBD in complex with Omi-6 and COVOX-150 Fabs
Components
  • COVOX-150 heavy chain
  • COVOX-150 light chain
  • Omi-6 heavy chain
  • Omi-6 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Omicron / BA.1 / BA.2 / RBD / antibody / Fab / Omi-6 / COVOX-150 / VIRAL PROTEIN/IMMUNE SYSTEM
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, 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, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.24 Å
AuthorsZhou, D. / Huo, J. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Cell / Year: 2022
Title: Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Authors: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / ...Authors: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / Donal Skelly / Thomas G Ritter / Ali Amini / Sagida Bibi / Sandra Adele / Sile Ann Johnson / Bede Constantinides / Hermione Webster / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / Derrick Crook / Andrew J Pollard / Teresa Lambe / Philip Goulder / / Neil G Paterson / Mark A Williams / David R Hall / Juthathip Mongkolsapaya / Elizabeth E Fry / Wanwisa Dejnirattisai / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA. ...Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.
History
DepositionApr 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Spike protein S1
B: Spike protein S1
C: Spike protein S1
A: Spike protein S1
E: Omi-6 heavy chain
F: Omi-6 light chain
K: Omi-6 light chain
M: Omi-6 heavy chain
N: Omi-6 light chain
L: Omi-6 light chain
X: COVOX-150 heavy chain
Y: COVOX-150 light chain
S: COVOX-150 heavy chain
T: COVOX-150 light chain
O: COVOX-150 heavy chain
P: COVOX-150 light chain
Q: COVOX-150 heavy chain
R: COVOX-150 light chain
J: Omi-6 heavy chain
H: Omi-6 heavy chain


Theoretical massNumber of molelcules
Total (without water)470,17820
Polymers470,17820
Non-polymers00
Water0
1
D: Spike protein S1
M: Omi-6 heavy chain
N: Omi-6 light chain
S: COVOX-150 heavy chain
T: COVOX-150 light chain


Theoretical massNumber of molelcules
Total (without water)117,5455
Polymers117,5455
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spike protein S1
E: Omi-6 heavy chain
F: Omi-6 light chain
O: COVOX-150 heavy chain
P: COVOX-150 light chain


Theoretical massNumber of molelcules
Total (without water)117,5455
Polymers117,5455
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Spike protein S1
K: Omi-6 light chain
X: COVOX-150 heavy chain
Y: COVOX-150 light chain
J: Omi-6 heavy chain


Theoretical massNumber of molelcules
Total (without water)117,5455
Polymers117,5455
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Spike protein S1
L: Omi-6 light chain
Q: COVOX-150 heavy chain
R: COVOX-150 light chain
H: Omi-6 heavy chain


Theoretical massNumber of molelcules
Total (without water)117,5455
Polymers117,5455
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.816, 114.783, 144.549
Angle α, β, γ (deg.)82.007, 80.620, 86.166
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 347 through 489 or resid 491...
d_2ens_1(chain "B" and (resid 347 through 448 or (resid 449...
d_3ens_1(chain "C" and (resid 347 through 489 or resid 491 through 492 or resid 494 through 527))
d_4ens_1(chain "D" and (resid 347 through 448 or (resid 449...
d_1ens_2(chain "F" and (resid 2 or resid 4 through 11...
d_2ens_2(chain "P" and (resid 2 or resid 4 through 11...
d_3ens_2(chain "R" and (resid 2 or resid 4 through 11...
d_4ens_2(chain "T" and (resid 2 or resid 4 through 11...
d_5ens_2(chain "Y" and (resid 2 or resid 4 through 11...
d_1ens_3(chain "H" and (resid 1 through 38 or (resid 39...
d_2ens_3chain "J"
d_3ens_3(chain "M" and (resid 1 through 38 or (resid 39...
d_1ens_4(chain "K" and (resid 1 through 39 or (resid 40...
d_2ens_4(chain "L" and (resid 1 through 31 or (resid 32...
d_3ens_4(chain "N" and (resid 1 through 136 or (resid 137...
d_1ens_5(chain "O" and resid 2 through 220)
d_2ens_5(chain "Q" and resid 2 through 220)
d_3ens_5(chain "S" and resid 2 through 220)
d_4ens_5(chain "X" and resid 2 through 220)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PHETYRD16 - 163
d_12ens_1PROLEUD165 - 166
d_13ens_1SERLYSD168 - 201
d_21ens_1PHETYRB16 - 163
d_22ens_1PROLEUB165 - 166
d_23ens_1SERLYSB168 - 201
d_31ens_1PHETYRC16 - 163
d_32ens_1PROLEUC165 - 166
d_33ens_1SERLYSC168 - 201
d_41ens_1PHETYRA16 - 163
d_42ens_1PROLEUA165 - 166
d_43ens_1SERLYSA168 - 201
d_11ens_2ILEILEF2
d_12ens_2METLEUF4 - 11
d_13ens_2ALAILEF13 - 21
d_14ens_2CYSALAF23 - 25
d_15ens_2GLNGLNF27
d_16ens_2ILESERF29 - 31
d_17ens_2LEULEUF33
d_18ens_2TRPLYSF35 - 39
d_19ens_2GLYTYRF41 - 49
d_110ens_2ALASERF51 - 52
d_111ens_2GLNALAF55 - 84
d_112ens_2TYRGLNF86 - 90
d_113ens_2THRGLYF99 - 101
d_114ens_2GLYILEF103 - 108
d_115ens_2GLNPROF126 - 143
d_116ens_2ALASERF146 - 164
d_117ens_2THRTHRF166
d_118ens_2GLNHISF168 - 191
d_119ens_2VALGLYF193 - 214
d_21ens_2ILEILEP2
d_22ens_2METLEUP4 - 11
d_23ens_2ALAILEP13 - 21
d_24ens_2CYSALAP23 - 25
d_25ens_2GLNGLNP27
d_26ens_2ILESERP29 - 31
d_27ens_2LEULEUP33
d_28ens_2TRPLYSP35 - 39
d_29ens_2GLYTYRP41 - 49
d_210ens_2ALASERP51 - 52
d_211ens_2GLNALAP55 - 84
d_212ens_2TYRGLNP86 - 90
d_213ens_2THRGLYP99 - 101
d_214ens_2GLYILEP103 - 108
d_215ens_2GLNPROP126 - 143
d_216ens_2ALASERP146 - 164
d_217ens_2THRTHRP166
d_218ens_2GLNHISP168 - 191
d_219ens_2VALGLYP193 - 214
d_31ens_2ILEILER2
d_32ens_2METLEUR4 - 11
d_33ens_2ALAILER13 - 21
d_34ens_2CYSALAR23 - 25
d_35ens_2GLNGLNR27
d_36ens_2ILESERR29 - 31
d_37ens_2LEULEUR33
d_38ens_2TRPLYSR35 - 39
d_39ens_2GLYTYRR41 - 49
d_310ens_2ALASERR51 - 52
d_311ens_2GLNALAR55 - 84
d_312ens_2TYRGLNR86 - 90
d_313ens_2THRGLYR99 - 101
d_314ens_2GLYILER103 - 108
d_315ens_2GLNPROR126 - 143
d_316ens_2ALASERR146 - 164
d_317ens_2THRTHRR166
d_318ens_2GLNHISR168 - 191
d_319ens_2VALGLYR193 - 214
d_41ens_2ILEILEN2
d_42ens_2METLEUN4 - 11
d_43ens_2ALAILEN13 - 21
d_44ens_2CYSALAN23 - 25
d_45ens_2GLNGLNN27
d_46ens_2ILESERN29 - 31
d_47ens_2LEULEUN33
d_48ens_2TRPLYSN35 - 39
d_49ens_2GLYTYRN41 - 49
d_410ens_2ALASERN51 - 52
d_411ens_2GLNALAN55 - 84
d_412ens_2TYRGLNN86 - 90
d_413ens_2THRGLYN99 - 101
d_414ens_2GLYILEN103 - 108
d_415ens_2GLNPRON126 - 143
d_416ens_2ALASERN146 - 164
d_417ens_2THRTHRN166
d_418ens_2GLNHISN168 - 191
d_419ens_2VALGLYN193 - 214
d_51ens_2ILEILEL2
d_52ens_2METLEUL4 - 11
d_53ens_2ALAILEL13 - 21
d_54ens_2CYSALAL23 - 25
d_55ens_2GLNGLNL27
d_56ens_2ILESERL29 - 31
d_57ens_2LEULEUL33
d_58ens_2TRPLYSL35 - 39
d_59ens_2GLYTYRL41 - 49
d_510ens_2ALASERL51 - 52
d_511ens_2GLNALAL55 - 84
d_512ens_2TYRGLNL86 - 90
d_513ens_2THRGLYL99 - 101
d_514ens_2GLYILEL103 - 108
d_515ens_2GLNPROL126 - 143
d_516ens_2ALASERL146 - 164
d_517ens_2THRTHRL166
d_518ens_2GLNHISL168 - 191
d_519ens_2VALGLYL193 - 214
d_11ens_3GLULYST1 - 225
d_21ens_3GLULYSS1 - 225
d_31ens_3GLULYSH1 - 225
d_11ens_4ALAASPG1 - 105
d_12ens_4THRARGG109 - 142
d_13ens_4ALAGLUG144 - 213
d_21ens_4ALAASPJ1 - 105
d_22ens_4THRARGJ109 - 142
d_23ens_4ALAGLUJ144 - 213
d_31ens_4ALAASPI1 - 105
d_32ens_4THRARGI109 - 142
d_33ens_4ALAGLUI144 - 213
d_11ens_5VALCYSO2 - 220
d_21ens_5VALCYSQ2 - 220
d_31ens_5VALCYSM2 - 220
d_41ens_5VALCYSK2 - 220

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(0.999934165519, -0.00945613169014, 0.00649970771016), (-0.00670427720644, -0.0217651302865, 0.99974063225), (-0.0093122120894, -0.999718390687, -0.0218270939186)-26.2229032164, -83.374175284, -94.1953305687
2given(0.994166888913, 0.107794577201, 0.00353922527184), (0.00949396098733, -0.0547785457721, -0.998453391815), (-0.107433987612, 0.992662903532, -0.05548241394)23.575746445, 16.1642566423, 55.4836256716
3given(0.999317148284, 0.0330280430151, 0.0165645863216), (0.0321110998202, -0.998085416067, 0.0528618908444), (0.0182787968355, -0.0522938869267, -0.998464438514)42.5308343133, -153.632487477, 98.5628133778
4given(0.830949432313, 0.0948008546037, 0.548211491038), (0.556342194145, -0.146073145905, -0.818013446747), (0.00253060328839, 0.984720992978, -0.174121113123)-6.91884848864, 5.03720601903, -9.80995646076
5given(0.825532117811, 0.0582602047318, 0.561339889022), (-0.0446153541584, -0.984806826611, 0.167824266522), (0.562588830885, -0.163588700114, -0.810390365539)17.74474462, -87.8659167787, 87.0097721613
6given(0.81953937884, 0.0343346891244, 0.571993300356), (0.06540691353, 0.986074179474, -0.152904049117), (-0.569277737306, 0.162723205772, 0.805880894494)58.2446022485, -62.3651228874, 14.943826421
7given(0.810237613805, -0.00492598424327, 0.586080833891), (-0.573851883533, 0.196705855988, 0.794984793557), (-0.119201614675, -0.980450172573, 0.156551698041)31.9727044842, -66.7488940579, -36.3706623002
8given(0.99503237934, 0.0991407518922, 0.00903744316962), (0.012153761571, -0.030874482102, -0.999449374623), (-0.098807136101, 0.994594328191, -0.0319260424473)22.4978415114, 18.9211354537, 53.3665727074
9given(0.999439141971, 0.0121987984511, 0.0311863882605), (0.00979850553298, -0.997060254491, 0.0759923562122), (0.0320217236529, -0.0756441552911, -0.996620575236)39.0116011027, -155.183641232, 96.9857700838
10given(0.995560335218, -0.00268794891066, -0.0940871610327), (0.0940037505074, -0.022441670571, 0.995318876699), (-0.00478683936324, -0.999744540547, -0.0220893597978)-17.9321765691, -54.2875512464, 20.4884612912
11given(0.994063280812, -0.0387941465606, -0.10165238774), (-0.103477828678, -0.0483691745631, -0.993454962202), (0.0336233953176, 0.998075867429, -0.0520963544078)19.6738274712, -100.045268364, 80.0572724352
12given(0.999851373368, -0.013464828233, -0.0107670597441), (-0.0108524768107, -0.00628682093597, -0.999921346722), (0.0133960786035, 0.999889581045, -0.00643201328311)24.313467845, -96.2194887692, 82.2641973776
13given(0.996926794636, -0.00489847339654, -0.0781854915959), (0.0782708188936, 0.0207163264304, 0.996716866883), (-0.00326267489029, -0.999773393714, 0.021036068429)64.642315487, -51.3159871628, 20.5142590269
14given(0.99366200344, -0.0196004418789, -0.110687151906), (-0.0134523158451, -0.998338949433, 0.0560212213743), (-0.111601335644, -0.0541771605386, -0.992275151941)37.883265531, -61.0120817612, -47.3208703497

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Components

#1: Protein
Spike protein S1 / SARS-CoV-2 Omicron Spike protein


Mass: 23157.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody
Omi-6 heavy chain


Mass: 24297.236 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
Omi-6 light chain


Mass: 23218.787 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody
COVOX-150 heavy chain


Mass: 23415.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody
COVOX-150 light chain


Mass: 23456.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium HEPES pH 7.0, 15 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 4.24→142 Å / Num. obs: 12518 / % possible obs: 82.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 57.8 Å2 / CC1/2: 0.918 / Rmerge(I) obs: 0.33 / Rpim(I) all: 0.205 / Net I/σ(I): 2.6
Reflection shellResolution: 4.243→4.736 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 626 / CC1/2: 0.59

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Processing

Software
NameVersionClassification
GDA1.19_4092data collection
PHENIX1.19_4092refinement
GDA1.19_4092data collection
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BEI

7bei


Resolution: 4.24→113.55 Å / SU ML: 0.6513 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.8422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2724 595 4.75 %
Rwork0.2369 11919 -
obs0.2385 12514 34.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.48 Å2
Refinement stepCycle: LAST / Resolution: 4.24→113.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31950 0 0 0 31950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007132691
X-RAY DIFFRACTIONf_angle_d0.966644484
X-RAY DIFFRACTIONf_chiral_restr0.05865051
X-RAY DIFFRACTIONf_plane_restr0.00715688
X-RAY DIFFRACTIONf_dihedral_angle_d11.571611596
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS0.175949161086
ens_1d_3CX-RAY DIFFRACTIONTorsion NCS0.162323626066
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.159177438031
ens_2d_2YX-RAY DIFFRACTIONTorsion NCS1.14425444526
ens_2d_3TX-RAY DIFFRACTIONTorsion NCS1.24345951013
ens_2d_4PX-RAY DIFFRACTIONTorsion NCS1.19686339843
ens_2d_5RX-RAY DIFFRACTIONTorsion NCS1.27493226747
ens_3d_2MX-RAY DIFFRACTIONTorsion NCS0.963771703716
ens_3d_3JX-RAY DIFFRACTIONTorsion NCS0.584273401686
ens_4d_2KX-RAY DIFFRACTIONTorsion NCS0.497452196235
ens_4d_3NX-RAY DIFFRACTIONTorsion NCS1.16178650553
ens_5d_2SX-RAY DIFFRACTIONTorsion NCS0.23976368015
ens_5d_3OX-RAY DIFFRACTIONTorsion NCS0.492319149932
ens_5d_4QX-RAY DIFFRACTIONTorsion NCS0.524483008781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.24-4.670.3394220.2606467X-RAY DIFFRACTION5.31
4.67-5.340.2964630.26221228X-RAY DIFFRACTION14.1
5.35-6.730.33321160.28192459X-RAY DIFFRACTION27.93
6.73-113.550.25463940.2237765X-RAY DIFFRACTION88.79
Refinement TLS params.Method: refined / Origin x: -18.8350616034 Å / Origin y: -52.9770122989 Å / Origin z: 16.2186864444 Å
111213212223313233
T0.53964346126 Å20.0755550210433 Å20.0231285609429 Å2-0.598293276654 Å20.0338265034247 Å2--0.573883086833 Å2
L0.119631138792 °20.0308702508611 °2-0.00931258063881 °2-0.151218651345 °2-0.10853568991 °2--0.204568004452 °2
S-0.00448889915282 Å °0.0745301067964 Å °-0.0548511751248 Å °0.0186440296947 Å °-0.0474792201105 Å °0.00795620620958 Å °-0.112266094054 Å °0.00710158644312 Å °-0.0149235049151 Å °
Refinement TLS groupSelection details: all

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