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- PDB-4dx9: ICAP1 in complex with integrin beta 1 cytoplasmic tail -

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Basic information

Entry
Database: PDB / ID: 4dx9
TitleICAP1 in complex with integrin beta 1 cytoplasmic tail
Components
  • Integrin beta-1
  • Integrin beta-1-binding protein 1
KeywordsPROTEIN BINDING / Protein-protein complex / PTB domain / Integrin binding / Integrin beta-1 / Membrane
Function / homology
Function and homology information


negative regulation of protein targeting to membrane / integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / myoblast fate specification / positive regulation of glutamate uptake involved in transmission of nerve impulse / regulation of inward rectifier potassium channel activity ...negative regulation of protein targeting to membrane / integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / myoblast fate specification / positive regulation of glutamate uptake involved in transmission of nerve impulse / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process / integrin alpha9-beta1 complex / regulation of integrin-mediated signaling pathway / cell-cell adhesion mediated by integrin / integrin alpha4-beta1 complex / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha1-beta1 complex / negative regulation of cell adhesion involved in substrate-bound cell migration / biomineral tissue development / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / regulation of synapse pruning / formation of radial glial scaffolds / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / reactive gliosis / cerebellar climbing fiber to Purkinje cell synapse / negative regulation of substrate adhesion-dependent cell spreading / myoblast migration / Other semaphorin interactions / CD40 signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / Fibronectin matrix formation / basement membrane organization / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / myelin sheath abaxonal region / CHL1 interactions / cardiac muscle cell myoblast differentiation / Laminin interactions / negative regulation of focal adhesion assembly / germ cell migration / tube formation / MET interacts with TNS proteins / leukocyte tethering or rolling / cardiac muscle cell differentiation / cell projection organization / integrin activation / Platelet Adhesion to exposed collagen / myoblast fusion / negative regulation of cell migration involved in sprouting angiogenesis / Elastic fibre formation / mesodermal cell differentiation / negative regulation of fibroblast migration / axon extension / cellular response to fibroblast growth factor stimulus / positive regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / wound healing, spreading of epidermal cells / regulation of spontaneous synaptic transmission / GDP-dissociation inhibitor activity / heterotypic cell-cell adhesion / myoblast differentiation / integrin complex / dendrite morphogenesis / Basigin interactions / muscle organ development / Molecules associated with elastic fibres / sarcomere organization / lamellipodium assembly / cell adhesion mediated by integrin / negative regulation of Rho protein signal transduction / MET activates PTK2 signaling / maintenance of blood-brain barrier / Syndecan interactions / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / positive regulation of neuroblast proliferation / positive regulation of wound healing / regulation of GTPase activity / receptor clustering / positive regulation of Notch signaling pathway / cell-substrate adhesion / homophilic cell adhesion via plasma membrane adhesion molecules / TGF-beta receptor signaling activates SMADs / positive regulation of focal adhesion assembly / establishment of mitotic spindle orientation / glial cell projection / cleavage furrow / regulation of cell adhesion mediated by integrin / positive regulation of cell division / cellular response to low-density lipoprotein particle stimulus / fibronectin binding / neuroblast proliferation / positive regulation of protein targeting to membrane / centriolar satellite / RHOG GTPase cycle / negative regulation of anoikis
Similarity search - Function
Omega-AgatoxinV / Omega-AgatoxinV - #10 / Integrin binding protein, ICAP-1 / Beta-1 integrin binding protein / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain ...Omega-AgatoxinV / Omega-AgatoxinV - #10 / Integrin binding protein, ICAP-1 / Beta-1 integrin binding protein / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / Integrin domain superfamily / Other non-globular / PSI domain / domain found in Plexins, Semaphorins and Integrins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / Special / Roll / Mainly Beta
Similarity search - Domain/homology
Integrin beta-1-binding protein 1 / Integrin beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.99 Å
AuthorsLiu, W. / Draheim, K. / Zhang, R. / Calderwood, D.A. / Boggon, T.J.
CitationJournal: Mol.Cell / Year: 2013
Title: Mechanism for KRIT1 Release of ICAP1-Mediated Suppression of Integrin Activation.
Authors: Liu, W. / Draheim, K.M. / Zhang, R. / Calderwood, D.A. / Boggon, T.J.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Mar 13, 2013Group: Database references
Revision 1.3Sep 2, 2020Group: Database references / Derived calculations / Structure summary
Category: struct_conn / struct_keywords / struct_ref_seq_dif
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_keywords.text / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin beta-1-binding protein 1
0: Integrin beta-1-binding protein 1
k: Integrin beta-1-binding protein 1
l: Integrin beta-1
m: Integrin beta-1-binding protein 1
n: Integrin beta-1
1: Integrin beta-1-binding protein 1
C: Integrin beta-1-binding protein 1
x: Integrin beta-1
D: Integrin beta-1
2: Integrin beta-1-binding protein 1
E: Integrin beta-1-binding protein 1
3: Integrin beta-1-binding protein 1
G: Integrin beta-1-binding protein 1
8: Integrin beta-1
H: Integrin beta-1
o: Integrin beta-1-binding protein 1
p: Integrin beta-1
q: Integrin beta-1-binding protein 1
B: Integrin beta-1
9: Integrin beta-1
F: Integrin beta-1
r: Integrin beta-1
I: Integrin beta-1-binding protein 1
4: Integrin beta-1-binding protein 1
J: Integrin beta-1
7: Integrin beta-1
K: Integrin beta-1-binding protein 1
5: Integrin beta-1-binding protein 1
L: Integrin beta-1
6: Integrin beta-1
M: Integrin beta-1-binding protein 1
N: Integrin beta-1
O: Integrin beta-1-binding protein 1
P: Integrin beta-1
a: Integrin beta-1-binding protein 1
s: Integrin beta-1-binding protein 1
t: Integrin beta-1
u: Integrin beta-1-binding protein 1
v: Integrin beta-1
b: Integrin beta-1
c: Integrin beta-1-binding protein 1
d: Integrin beta-1
e: Integrin beta-1-binding protein 1
f: Integrin beta-1
g: Integrin beta-1-binding protein 1
h: Integrin beta-1
i: Integrin beta-1-binding protein 1
j: Integrin beta-1
Q: Integrin beta-1-binding protein 1
R: Integrin beta-1
S: Integrin beta-1-binding protein 1
T: Integrin beta-1
U: Integrin beta-1-binding protein 1
V: Integrin beta-1
W: Integrin beta-1-binding protein 1
w: Integrin beta-1-binding protein 1
X: Integrin beta-1
Y: Integrin beta-1-binding protein 1
y: Integrin beta-1-binding protein 1
Z: Integrin beta-1
z: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)601,36162
Polymers601,36162
Non-polymers00
Water0
1
A: Integrin beta-1-binding protein 1
B: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Integrin beta-1-binding protein 1
D: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Integrin beta-1-binding protein 1
F: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Integrin beta-1-binding protein 1
H: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Integrin beta-1-binding protein 1
J: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Integrin beta-1-binding protein 1
L: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Integrin beta-1-binding protein 1
N: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: Integrin beta-1-binding protein 1
P: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
Q: Integrin beta-1-binding protein 1
R: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
S: Integrin beta-1-binding protein 1
T: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
U: Integrin beta-1-binding protein 1
V: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
W: Integrin beta-1-binding protein 1
X: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
Y: Integrin beta-1-binding protein 1
Z: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
a: Integrin beta-1-binding protein 1
b: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
c: Integrin beta-1-binding protein 1
d: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
e: Integrin beta-1-binding protein 1
f: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
g: Integrin beta-1-binding protein 1
h: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
i: Integrin beta-1-binding protein 1
j: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
19
k: Integrin beta-1-binding protein 1
l: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
20
m: Integrin beta-1-binding protein 1
n: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
21
o: Integrin beta-1-binding protein 1
p: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
22
2: Integrin beta-1-binding protein 1
r: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
23
s: Integrin beta-1-binding protein 1
t: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
24
u: Integrin beta-1-binding protein 1
v: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
25
1: Integrin beta-1-binding protein 1
x: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
26
y: Integrin beta-1-binding protein 1
z: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
27
3: Integrin beta-1-binding protein 1
8: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
28
5: Integrin beta-1-binding protein 1
6: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
29
0: Integrin beta-1-binding protein 1
9: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
30
4: Integrin beta-1-binding protein 1
7: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)18,8942
Polymers18,8942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
31
q: Integrin beta-1-binding protein 1


Theoretical massNumber of molelcules
Total (without water)17,2701
Polymers17,2701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
32
w: Integrin beta-1-binding protein 1


Theoretical massNumber of molelcules
Total (without water)17,2701
Polymers17,2701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.622, 122.207, 135.269
Angle α, β, γ (deg.)89.97, 89.99, 108.11
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11M
21S
31U
41W
51Y
61g
12Q
22a
32k
42s
13c
23e
33m
43u
53y

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112M60 - 72
2112S60 - 72
3112U60 - 72
4112W60 - 72
5112Y60 - 72
6112g60 - 72
1212M86 - 115
2212S86 - 115
3212U86 - 115
4212W86 - 115
5212Y86 - 115
6212g86 - 115
1312M119 - 124
2312S119 - 124
3312U119 - 124
4312W119 - 124
5312Y119 - 124
6312g119 - 124
1412M126 - 194
2412S126 - 194
3412U126 - 194
4412W126 - 194
5412Y126 - 194
6412g126 - 194
1122Q60 - 71
2122a60 - 71
3122k60 - 71
4122s60 - 71
1222Q84 - 102
2222a84 - 102
3222k84 - 102
4222s84 - 102
1322Q105 - 115
2322a105 - 115
3322k105 - 115
4322s105 - 115
1422Q130 - 146
2422a130 - 146
3422k130 - 146
4422s130 - 146
1522Q167 - 189
2522a167 - 189
3522k167 - 189
4522s167 - 189
1132c60 - 71
2132e60 - 71
3132m60 - 71
4132u60 - 71
5132y60 - 71
1232c100 - 121
2232e100 - 121
3232m100 - 121
4232u100 - 121
5232y100 - 121
1332c130 - 160
2332e130 - 160
3332m130 - 160
4332u130 - 160
5332y130 - 160
1432c164 - 190
2432e164 - 190
3432m164 - 190
4432u164 - 190
5432y164 - 190

NCS ensembles :
ID
1
2
3

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Components

#1: Protein ...
Integrin beta-1-binding protein 1 / Integrin cytoplasmic domain-associated protein 1 / ICAP-1


Mass: 17270.154 Da / Num. of mol.: 32 / Fragment: PTB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ICAP1, Integrin cytoplasmic domain-associated protein 1 (ICAP1), ITGB1BP1
Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14713
#2: Protein/peptide ...
Integrin beta-1 / Fibronectin receptor subunit beta / VLA-4 subunit beta


Mass: 1623.867 Da / Num. of mol.: 30 / Fragment: Cytoplasmic tail / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05556

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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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.2M sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2011
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.273
11-h,-k,l20.239
11h,-h-k,-l30.248
11-H, H+K, -L40.239
ReflectionResolution: 2.99→50.01 Å / Num. all: 91718 / Num. obs: 91718 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Rsym value: 0.134 / Net I/σ(I): 16.6
Reflection shellResolution: 2.99→3.11 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 2.3 / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.99→50.01 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.836 / Occupancy max: 1 / Occupancy min: 1 / SU B: 42.591 / SU ML: 0.506 / Cross valid method: THROUGHOUT / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.31194 5056 5.6 %RANDOM
Rwork0.25129 ---
obs0.2546 85975 98.2 %-
all-91031 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.204 Å2
Baniso -1Baniso -2Baniso -3
1-5.85 Å23.25 Å211.87 Å2
2--53.99 Å211.38 Å2
3----59.84 Å2
Refinement stepCycle: LAST / Resolution: 2.99→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29306 0 0 0 29306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0229715
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8131.98640083
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.98253588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52625.0461195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.111155026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2061589
X-RAY DIFFRACTIONr_chiral_restr0.0470.24759
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02121275
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.99→3.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 635 -
Rwork0.22 5512 -
obs--89.83 %
Refinement TLS params.

Method: 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)
10.16410.15630.3690.16210.37360.874-0.0370.00720.0734-0.0639-0.0053-0.0068-0.1708-0.02770.04230.48730.02350.00760.16570.13050.543133.3906101.5246-51.1161
20.5495-0.3776-0.15190.40530.12730.0654-0.02380.04520.02040.07060.01920.0531-0.02590.05140.00460.32260.04320.07290.27460.08810.6233-8.5189.2514-55.5312
30.0269-0.0431-0.06230.63250.19070.17840.02010.0151-0.02930.0207-0.0410.03250.0168-0.02970.02090.24830.0660.01410.33830.1080.50127.669544.0924-95.5681
40.084-0.09310.01080.43010.00150.0067-0.00880.0168-0.0167-0.01850.0395-0.02450.01960.0237-0.03060.3760.07150.04870.29510.06760.437929.861321.083-79.7329
50.6141-0.5769-0.35040.7660.26170.32220.0057-0.01520.0469-0.02170.0425-0.0485-0.13280.0861-0.04820.24570.00990.01020.33810.08320.5187-19.208871.24-50.2018
60.0115-0.293-0.10028.26982.84490.9821-0.1456-0.01540.0058-1.27770.3742-0.1014-0.45320.1556-0.22860.3801-0.01310.0230.61980.20340.101-6.559549.5632-50.624
70.82660.35570.20570.17220.05220.2183-0.1048-0.06490.0754-0.00470.01220.0405-0.0704-0.10380.09260.2410.09360.0280.24720.13080.49569.158660.8298-27.3388
831.89969.54283.58752.96361.15382.52380.8329-0.88821.04330.3565-0.45220.2075-0.0713-0.2813-0.38080.3136-0.12250.08870.27050.16260.291531.486491.2092-28.1788
90.51780.75880.29511.9686-0.08231.27890.0368-0.0540.0737-0.0779-0.0367-0.11080.12460.0233-0.00010.29380.06610.01620.22810.07320.4887-19.749744.342-74.0398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 194
2X-RAY DIFFRACTION1060 - 196
3X-RAY DIFFRACTION2C60 - 195
4X-RAY DIFFRACTION2160 - 193
5X-RAY DIFFRACTION3E60 - 194
6X-RAY DIFFRACTION3260 - 196
7X-RAY DIFFRACTION4G60 - 195
8X-RAY DIFFRACTION4360 - 190
9X-RAY DIFFRACTION5I60 - 194
10X-RAY DIFFRACTION5459 - 196
11X-RAY DIFFRACTION6J784 - 794
12X-RAY DIFFRACTION7K60 - 192
13X-RAY DIFFRACTION7559 - 196
14X-RAY DIFFRACTION86784 - 794
15X-RAY DIFFRACTION9M60 - 195

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