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- PDB-7q5u: The tandem SH2 domains of SYK with a bound CD3G diphospho-ITAM peptide -

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Basic information

Entry
Database: PDB / ID: 7q5u
TitleThe tandem SH2 domains of SYK with a bound CD3G diphospho-ITAM peptide
Components
  • T-cell surface glycoprotein CD3 gamma chain
  • Tyrosine-protein kinase SYK
KeywordsTRANSFERASE / Signalling / kinase
Function / homology
Function and homology information


regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / serotonin secretion by platelet / interleukin-15 receptor binding / positive regulation of interleukin-3 production / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonic acid secretion / cellular response to lectin / gamma-delta T cell differentiation ...regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / serotonin secretion by platelet / interleukin-15 receptor binding / positive regulation of interleukin-3 production / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonic acid secretion / cellular response to lectin / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / B cell receptor complex / neutrophil activation involved in immune response / Toll-like receptor binding / regulation of platelet aggregation / positive regulation of alpha-beta T cell proliferation / leukocyte activation involved in immune response / positive regulation of mast cell cytokine production / gamma-delta T cell activation / regulation of platelet activation / lymph vessel development / collagen-activated tyrosine kinase receptor signaling pathway / cell activation / positive regulation of mast cell degranulation / alpha-beta T cell receptor complex / macrophage activation involved in immune response / beta selection / regulation of phagocytosis / positive thymic T cell selection / positive regulation of killing of cells of another organism / leukotriene biosynthetic process / cellular response to molecule of fungal origin / regulation of tumor necrosis factor-mediated signaling pathway / FLT3 signaling through SRC family kinases / early phagosome / interleukin-3-mediated signaling pathway / cellular response to lipid / positive regulation of monocyte chemotactic protein-1 production / regulation of DNA-binding transcription factor activity / positive regulation of cell adhesion mediated by integrin / positive regulation of granulocyte macrophage colony-stimulating factor production / Fc epsilon receptor (FCERI) signaling / Interleukin-2 signaling / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / T cell receptor complex / positive regulation of B cell differentiation / leukocyte cell-cell adhesion / establishment or maintenance of cell polarity / mast cell degranulation / Fc-gamma receptor signaling pathway involved in phagocytosis / Dectin-2 family / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / phospholipase binding / positive regulation of interleukin-10 production / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of receptor internalization / cellular response to low-density lipoprotein particle stimulus / alpha-beta T cell activation / Generation of second messenger molecules / FCGR activation / PD-1 signaling / positive regulation of type I interferon production / positive regulation of interleukin-4 production / positive regulation of bone resorption / phosphatase binding / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of calcium-mediated signaling / Signaling by CSF3 (G-CSF) / negative regulation of inflammatory response to antigenic stimulus / GPVI-mediated activation cascade / positive regulation of TORC1 signaling / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of interleukin-12 production / phosphotyrosine residue binding / SH2 domain binding / T cell receptor binding / T cell activation / Integrin signaling / FCERI mediated Ca+2 mobilization / neutrophil chemotaxis / regulation of ERK1 and ERK2 cascade / B cell differentiation / FCGR3A-mediated IL10 synthesis / positive regulation of superoxide anion generation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / integrin-mediated signaling pathway / positive regulation of interleukin-8 production / calcium-mediated signaling / Regulation of signaling by CBL / positive regulation of protein-containing complex assembly / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / animal organ morphogenesis / B cell receptor signaling pathway / non-specific protein-tyrosine kinase
Similarity search - Function
CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain ...CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / T-cell surface glycoprotein CD3 gamma chain / Tyrosine-protein kinase SYK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Chen, Z. / Bountra, C. / von Delft, F. / Gileadi, O. / Brennan, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)5U54AG065187-03 United States
CitationJournal: To Be Published
Title: The tandem SH2 domains of SYK
Authors: Bradshaw, W.J. / Katis, V.L. / Chen, Z. / Bountra, C. / von Delft, F. / Gileadi, O. / Brennan, P.E.
History
DepositionNov 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Tyrosine-protein kinase SYK
BBB: Tyrosine-protein kinase SYK
CCC: Tyrosine-protein kinase SYK
DDD: Tyrosine-protein kinase SYK
EEE: Tyrosine-protein kinase SYK
FFF: Tyrosine-protein kinase SYK
GGG: T-cell surface glycoprotein CD3 gamma chain
HHH: T-cell surface glycoprotein CD3 gamma chain
III: T-cell surface glycoprotein CD3 gamma chain
JJJ: T-cell surface glycoprotein CD3 gamma chain
KKK: T-cell surface glycoprotein CD3 gamma chain
LLL: T-cell surface glycoprotein CD3 gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,17023
Polymers195,11112
Non-polymers1,05911
Water11,043613
1
AAA: Tyrosine-protein kinase SYK
LLL: T-cell surface glycoprotein CD3 gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9116
Polymers32,5192
Non-polymers3924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-8 kcal/mol
Surface area15000 Å2
MethodPISA
2
BBB: Tyrosine-protein kinase SYK
III: T-cell surface glycoprotein CD3 gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6253
Polymers32,5192
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-9 kcal/mol
Surface area14990 Å2
MethodPISA
3
CCC: Tyrosine-protein kinase SYK
JJJ: T-cell surface glycoprotein CD3 gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6434
Polymers32,5192
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-7 kcal/mol
Surface area14820 Å2
MethodPISA
4
DDD: Tyrosine-protein kinase SYK
HHH: T-cell surface glycoprotein CD3 gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5813
Polymers32,5192
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-10 kcal/mol
Surface area14920 Å2
MethodPISA
5
EEE: Tyrosine-protein kinase SYK
KKK: T-cell surface glycoprotein CD3 gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7874
Polymers32,5192
Non-polymers2682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-9 kcal/mol
Surface area14850 Å2
MethodPISA
6
FFF: Tyrosine-protein kinase SYK
GGG: T-cell surface glycoprotein CD3 gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6253
Polymers32,5192
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-10 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.321, 129.312, 95.346
Angle α, β, γ (deg.)90.000, 100.232, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74AAA
84EEE
95AAA
105FFF
116BBB
126CCC
137BBB
147DDD
158BBB
168EEE
179BBB
189FFF
1910CCC
2010DDD
2111CCC
2211EEE
2312CCC
2412FFF
2513DDD
2613EEE
2714DDD
2814FFF
2915EEE
3015FFF
3116GGG
3216HHH
3317GGG
3417III
3518GGG
3618JJJ
3719GGG
3819KKK
3920GGG
4020LLL
4121HHH
4221III
4322HHH
4422JJJ
4523HHH
4623KKK
4724HHH
4824LLL
4925III
5025JJJ
5126III
5226KKK
5327III
5427LLL
5528JJJ
5628KKK
5729JJJ
5829LLL
5930KKK
6030LLL

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERILEILEAAAA5 - 2621 - 258
221SERSERILEILEBBBB5 - 2621 - 258
332SERSERLYSLYSAAAA5 - 2611 - 257
442SERSERLYSLYSCCCC5 - 2611 - 257
553SERSERILEILEAAAA5 - 2621 - 258
663SERSERILEILEDDDD5 - 2621 - 258
774SERSERGLNGLNAAAA5 - 2601 - 256
884SERSERGLNGLNEEEE5 - 2601 - 256
995SERSERILEILEAAAA5 - 2621 - 258
10105SERSERILEILEFFFF5 - 2621 - 258
11116SERSERLYSLYSBBBB5 - 2611 - 257
12126SERSERLYSLYSCCCC5 - 2611 - 257
13137SERSERILEILEBBBB5 - 2621 - 258
14147SERSERILEILEDDDD5 - 2621 - 258
15158SERSERGLNGLNBBBB5 - 2601 - 256
16168SERSERGLNGLNEEEE5 - 2601 - 256
17179SERSERILEILEBBBB5 - 2621 - 258
18189SERSERILEILEFFFF5 - 2621 - 258
191910SERSERLYSLYSCCCC5 - 2611 - 257
202010SERSERLYSLYSDDDD5 - 2611 - 257
212111SERSERGLNGLNCCCC5 - 2601 - 256
222211SERSERGLNGLNEEEE5 - 2601 - 256
232312SERSERLYSLYSCCCC5 - 2611 - 257
242412SERSERLYSLYSFFFF5 - 2611 - 257
252513SERSERGLNGLNDDDD5 - 2601 - 256
262613SERSERGLNGLNEEEE5 - 2601 - 256
272714SERSERILEILEDDDD5 - 2621 - 258
282814SERSERILEILEFFFF5 - 2621 - 258
292915SERSERGLNGLNEEEE5 - 2601 - 256
303015SERSERGLNGLNFFFF5 - 2601 - 256
313116GLNGLNGLNGLNGGGG158 - 1752 - 19
323216GLNGLNGLNGLNHHHH158 - 1752 - 19
333317GLNGLNGLNGLNGGGG158 - 1752 - 19
343417GLNGLNGLNGLNIIII158 - 1752 - 19
353518GLNGLNGLNGLNGGGG158 - 1752 - 19
363618GLNGLNGLNGLNJJJJ158 - 1752 - 19
373719GLNGLNGLNGLNGGGG158 - 1752 - 19
383819GLNGLNGLNGLNKKKK158 - 1752 - 19
393920GLNGLNLEULEUGGGG158 - 1742 - 18
404020GLNGLNLEULEULLLL158 - 1742 - 18
414121GLNGLNGLNGLNHHHH158 - 1752 - 19
424221GLNGLNGLNGLNIIII158 - 1752 - 19
434322GLNGLNGLNGLNHHHH158 - 1752 - 19
444422GLNGLNGLNGLNJJJJ158 - 1752 - 19
454523GLNGLNGLNGLNHHHH158 - 1752 - 19
464623GLNGLNGLNGLNKKKK158 - 1752 - 19
474724GLNGLNLEULEUHHHH158 - 1742 - 18
484824GLNGLNLEULEULLLL158 - 1742 - 18
494925GLNGLNGLNGLNIIII158 - 1752 - 19
505025GLNGLNGLNGLNJJJJ158 - 1752 - 19
515126GLNGLNGLNGLNIIII158 - 1752 - 19
525226GLNGLNGLNGLNKKKK158 - 1752 - 19
535327GLNGLNLEULEUIIII158 - 1742 - 18
545427GLNGLNLEULEULLLL158 - 1742 - 18
555528GLNGLNGLNGLNJJJJ158 - 1752 - 19
565628GLNGLNGLNGLNKKKK158 - 1752 - 19
575729GLNGLNLEULEUJJJJ158 - 1742 - 18
585829GLNGLNLEULEULLLL158 - 1742 - 18
595930GLNGLNLEULEUKKKK158 - 1742 - 18
606030GLNGLNLEULEULLLL158 - 1742 - 18

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56
29Local NCS retraints between domains: 57 58
30Local NCS retraints between domains: 59 60

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Components

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Protein / Protein/peptide , 2 types, 12 molecules AAABBBCCCDDDEEEFFFGGGHHHIIIJJJKKKLLL

#1: Protein
Tyrosine-protein kinase SYK / / Spleen tyrosine kinase / p72-Syk


Mass: 29906.971 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P43405, non-specific protein-tyrosine kinase
#2: Protein/peptide
T-cell surface glycoprotein CD3 gamma chain / T-cell receptor T3 gamma chain


Mass: 2611.539 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P09693

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Non-polymers , 4 types, 624 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Diethylene glycol diethyl ether


Mass: 162.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100 mM MMT buffer, 30% PEG 1000

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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: May 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→93.83 Å / Num. obs: 86011 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.116 / Rrim(I) all: 0.25 / Χ2: 0.95 / Net I/σ(I): 7.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 9.3 % / Rmerge(I) obs: 2.507 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4550 / CC1/2: 0.395 / Rpim(I) all: 1.317 / Rrim(I) all: 2.849 / Χ2: 0.93 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A81

1a81


Resolution: 2.4→93.83 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.087 / SU ML: 0.253 / Cross valid method: FREE R-VALUE / ESU R: 0.373 / ESU R Free: 0.256
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2588 1977 2.301 %
Rwork0.2165 83930 -
all0.218 --
obs-85907 99.878 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.203 Å2
Baniso -1Baniso -2Baniso -3
1--1.589 Å20 Å2-1.88 Å2
2---0.554 Å2-0 Å2
3---2.649 Å2
Refinement stepCycle: LAST / Resolution: 2.4→93.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13363 0 70 613 14046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01313742
X-RAY DIFFRACTIONr_bond_other_d0.0010.01512947
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.64818519
X-RAY DIFFRACTIONr_angle_other_deg1.2341.58629874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.29451650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.95822.669753
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.932152433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0251584
X-RAY DIFFRACTIONr_chiral_restr0.0670.21681
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023186
X-RAY DIFFRACTIONr_nbd_refined0.2050.22546
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.211334
X-RAY DIFFRACTIONr_nbtor_refined0.1620.26294
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.26633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2521
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1010.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1470.251
X-RAY DIFFRACTIONr_nbd_other0.2020.2170
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2880.27
X-RAY DIFFRACTIONr_mcbond_it4.2024.5516622
X-RAY DIFFRACTIONr_mcbond_other4.2014.556620
X-RAY DIFFRACTIONr_mcangle_it6.3986.818258
X-RAY DIFFRACTIONr_mcangle_other6.3986.818258
X-RAY DIFFRACTIONr_scbond_it4.5874.9647120
X-RAY DIFFRACTIONr_scbond_other4.5864.9647121
X-RAY DIFFRACTIONr_scangle_it7.1077.23110258
X-RAY DIFFRACTIONr_scangle_other7.1077.23210259
X-RAY DIFFRACTIONr_lrange_it9.64350.98914749
X-RAY DIFFRACTIONr_lrange_other9.64851.01814668
X-RAY DIFFRACTIONr_ncsr_local_group_10.1030.057795
X-RAY DIFFRACTIONr_ncsr_local_group_20.0990.057790
X-RAY DIFFRACTIONr_ncsr_local_group_30.0930.057824
X-RAY DIFFRACTIONr_ncsr_local_group_40.0740.058012
X-RAY DIFFRACTIONr_ncsr_local_group_50.1060.057770
X-RAY DIFFRACTIONr_ncsr_local_group_60.0630.058146
X-RAY DIFFRACTIONr_ncsr_local_group_70.0950.057899
X-RAY DIFFRACTIONr_ncsr_local_group_80.1010.057785
X-RAY DIFFRACTIONr_ncsr_local_group_90.1010.057866
X-RAY DIFFRACTIONr_ncsr_local_group_100.0930.057914
X-RAY DIFFRACTIONr_ncsr_local_group_110.10.057817
X-RAY DIFFRACTIONr_ncsr_local_group_120.0970.057884
X-RAY DIFFRACTIONr_ncsr_local_group_130.0950.057789
X-RAY DIFFRACTIONr_ncsr_local_group_140.0830.057988
X-RAY DIFFRACTIONr_ncsr_local_group_150.0990.057791
X-RAY DIFFRACTIONr_ncsr_local_group_160.1610.05384
X-RAY DIFFRACTIONr_ncsr_local_group_170.1450.05393
X-RAY DIFFRACTIONr_ncsr_local_group_180.0820.05397
X-RAY DIFFRACTIONr_ncsr_local_group_190.0960.05399
X-RAY DIFFRACTIONr_ncsr_local_group_200.1490.05370
X-RAY DIFFRACTIONr_ncsr_local_group_210.1890.05379
X-RAY DIFFRACTIONr_ncsr_local_group_220.1390.05394
X-RAY DIFFRACTIONr_ncsr_local_group_230.1320.05395
X-RAY DIFFRACTIONr_ncsr_local_group_240.1170.05364
X-RAY DIFFRACTIONr_ncsr_local_group_250.1340.05392
X-RAY DIFFRACTIONr_ncsr_local_group_260.1510.05391
X-RAY DIFFRACTIONr_ncsr_local_group_270.1660.05359
X-RAY DIFFRACTIONr_ncsr_local_group_280.0860.05406
X-RAY DIFFRACTIONr_ncsr_local_group_290.1470.05361
X-RAY DIFFRACTIONr_ncsr_local_group_300.1260.05367
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.103260.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.103260.05008
23AAAX-RAY DIFFRACTIONLocal ncs0.098930.05008
24CCCX-RAY DIFFRACTIONLocal ncs0.098930.05008
35AAAX-RAY DIFFRACTIONLocal ncs0.093450.05008
36DDDX-RAY DIFFRACTIONLocal ncs0.093450.05008
47AAAX-RAY DIFFRACTIONLocal ncs0.073820.05009
48EEEX-RAY DIFFRACTIONLocal ncs0.073820.05009
59AAAX-RAY DIFFRACTIONLocal ncs0.106410.05008
510FFFX-RAY DIFFRACTIONLocal ncs0.106410.05008
611BBBX-RAY DIFFRACTIONLocal ncs0.062510.05009
612CCCX-RAY DIFFRACTIONLocal ncs0.062510.05009
713BBBX-RAY DIFFRACTIONLocal ncs0.094930.05008
714DDDX-RAY DIFFRACTIONLocal ncs0.094930.05008
815BBBX-RAY DIFFRACTIONLocal ncs0.100610.05008
816EEEX-RAY DIFFRACTIONLocal ncs0.100610.05008
917BBBX-RAY DIFFRACTIONLocal ncs0.1010.05008
918FFFX-RAY DIFFRACTIONLocal ncs0.1010.05008
1019CCCX-RAY DIFFRACTIONLocal ncs0.093220.05008
1020DDDX-RAY DIFFRACTIONLocal ncs0.093220.05008
1121CCCX-RAY DIFFRACTIONLocal ncs0.100460.05008
1122EEEX-RAY DIFFRACTIONLocal ncs0.100460.05008
1223CCCX-RAY DIFFRACTIONLocal ncs0.097350.05008
1224FFFX-RAY DIFFRACTIONLocal ncs0.097350.05008
1325DDDX-RAY DIFFRACTIONLocal ncs0.094650.05008
1326EEEX-RAY DIFFRACTIONLocal ncs0.094650.05008
1427DDDX-RAY DIFFRACTIONLocal ncs0.083320.05009
1428FFFX-RAY DIFFRACTIONLocal ncs0.083320.05009
1529EEEX-RAY DIFFRACTIONLocal ncs0.099420.05008
1530FFFX-RAY DIFFRACTIONLocal ncs0.099420.05008
1631GGGX-RAY DIFFRACTIONLocal ncs0.160970.05005
1632HHHX-RAY DIFFRACTIONLocal ncs0.160970.05005
1733GGGX-RAY DIFFRACTIONLocal ncs0.144980.05005
1734IIIX-RAY DIFFRACTIONLocal ncs0.144980.05005
1835GGGX-RAY DIFFRACTIONLocal ncs0.08250.05006
1836JJJX-RAY DIFFRACTIONLocal ncs0.08250.05006
1937GGGX-RAY DIFFRACTIONLocal ncs0.096430.05006
1938KKKX-RAY DIFFRACTIONLocal ncs0.096430.05006
2039GGGX-RAY DIFFRACTIONLocal ncs0.148530.05006
2040LLLX-RAY DIFFRACTIONLocal ncs0.148530.05006
2141HHHX-RAY DIFFRACTIONLocal ncs0.189290.05004
2142IIIX-RAY DIFFRACTIONLocal ncs0.189290.05004
2243HHHX-RAY DIFFRACTIONLocal ncs0.139010.05005
2244JJJX-RAY DIFFRACTIONLocal ncs0.139010.05005
2345HHHX-RAY DIFFRACTIONLocal ncs0.132090.05005
2346KKKX-RAY DIFFRACTIONLocal ncs0.132090.05005
2447HHHX-RAY DIFFRACTIONLocal ncs0.117320.05005
2448LLLX-RAY DIFFRACTIONLocal ncs0.117320.05005
2549IIIX-RAY DIFFRACTIONLocal ncs0.133940.05006
2550JJJX-RAY DIFFRACTIONLocal ncs0.133940.05006
2651IIIX-RAY DIFFRACTIONLocal ncs0.150970.05005
2652KKKX-RAY DIFFRACTIONLocal ncs0.150970.05005
2753IIIX-RAY DIFFRACTIONLocal ncs0.165620.05005
2754LLLX-RAY DIFFRACTIONLocal ncs0.165620.05005
2855JJJX-RAY DIFFRACTIONLocal ncs0.086070.05006
2856KKKX-RAY DIFFRACTIONLocal ncs0.086070.05006
2957JJJX-RAY DIFFRACTIONLocal ncs0.147460.05005
2958LLLX-RAY DIFFRACTIONLocal ncs0.147460.05005
3059KKKX-RAY DIFFRACTIONLocal ncs0.126410.05006
3060LLLX-RAY DIFFRACTIONLocal ncs0.126410.05006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.3521480.34961390.34962950.5270.52299.87290.346
2.462-2.530.3761230.31760600.31861900.6830.70899.88690.31
2.53-2.6030.3361300.3158710.31160080.7420.73699.88350.298
2.603-2.6830.2951370.27657090.27658520.7950.82899.89750.258
2.683-2.7710.3361370.27655130.27856550.80.8199.91160.257
2.771-2.8680.3011060.27553590.27654690.8120.82599.92690.25
2.868-2.9760.3131040.25351900.25452970.8580.86599.94340.228
2.976-3.0980.2821030.24149760.24250810.8810.89299.96060.217
3.098-3.2350.261220.22547350.22648600.9080.90999.93830.203
3.235-3.3930.2761000.21945870.2246910.9070.92299.91470.202
3.393-3.5760.251990.21243350.21344370.9160.92699.93240.197
3.576-3.7930.269960.22341040.22442030.9130.91399.92860.206
3.793-4.0540.2611140.19538330.19739490.9160.93199.94940.181
4.054-4.3780.2131030.15535880.15736920.9480.95999.97290.146
4.378-4.7950.169920.14733180.14834100.9620.9671000.141
4.795-5.360.242880.16729790.16930830.9510.96599.4810.163
5.36-6.1850.292600.18726170.18927030.9410.9699.03810.182
6.185-7.5670.198410.16922740.1723180.9450.95699.87060.165
7.567-10.6670.178430.16117540.16117970.9640.9671000.162
10.667-93.830.258310.2379890.23810220.9520.92799.80430.259

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