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- PDB-3ze2: Integrin alphaIIB beta3 headpiece and RGD peptide complex -

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Basic information

Entry
Database: PDB / ID: 3ze2
TitleIntegrin alphaIIB beta3 headpiece and RGD peptide complex
Components
  • 10E5 FAB HEAVY CHAIN
  • 10E5 FAB LIGHT CHAIN
  • INTEGRIN ALPHA-IIB
  • INTEGRIN BETA-3
  • RGD PEPTIDE
KeywordsCELL ADHESION/IMMUNE SYSTEM/PEPTIDE / CELL ADHESION-IMMUNE SYSTEM-PEPTIDE COMPLEX / CELL ADHESIN-IMMUNE SYSTEM-PEPTIDE COMPLEX / CELL ADHESION
Function / homology
Function and homology information


tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization ...tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / glycinergic synapse / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / : / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / angiogenesis involved in wound healing / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / positive regulation of leukocyte migration / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / smooth muscle cell migration / Molecules associated with elastic fibres / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / negative chemotaxis / cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / Syndecan interactions / microvillus membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of osteoblast proliferation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / positive regulation of bone resorption / positive regulation of T cell migration / negative regulation of endothelial cell apoptotic process / coreceptor activity / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / Integrin signaling / embryo implantation / substrate adhesion-dependent cell spreading / protein kinase C binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / Signal transduction by L1 / response to activity / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / wound healing / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cell-cell adhesion / platelet activation / VEGFA-VEGFR2 Pathway / platelet aggregation / ruffle membrane / cellular response to mechanical stimulus / positive regulation of fibroblast proliferation / positive regulation of angiogenesis / Signaling by RAF1 mutants
Similarity search - Function
ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / ligand-binding face of the semaphorins, domain 2 / Integrin alpha, N-terminal / 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 ...ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / ligand-binding face of the semaphorins, domain 2 / Integrin alpha, N-terminal / 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 alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsZhu, J.H. / Zhu, J.Q. / Springer, T.A.
CitationJournal: J.Cell Biol. / Year: 2013
Title: Complete Integrin Headpiece Opening in Eight Steps.
Authors: Zhu, J. / Zhu, J. / Springer, T.A.
History
DepositionDec 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTEGRIN ALPHA-IIB
B: INTEGRIN BETA-3
C: INTEGRIN ALPHA-IIB
D: INTEGRIN BETA-3
E: 10E5 FAB HEAVY CHAIN
F: 10E5 FAB LIGHT CHAIN
H: 10E5 FAB HEAVY CHAIN
I: RGD PEPTIDE
J: RGD PEPTIDE
L: 10E5 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,81440
Polymers298,58310
Non-polymers4,23130
Water23,7441318
1
A: INTEGRIN ALPHA-IIB
B: INTEGRIN BETA-3
E: 10E5 FAB HEAVY CHAIN
F: 10E5 FAB LIGHT CHAIN
I: RGD PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,76721
Polymers149,2925
Non-polymers2,47516
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11890 Å2
ΔGint-57.1 kcal/mol
Surface area67940 Å2
MethodPISA
2
C: INTEGRIN ALPHA-IIB
D: INTEGRIN BETA-3
H: 10E5 FAB HEAVY CHAIN
J: RGD PEPTIDE
L: 10E5 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,04719
Polymers149,2925
Non-polymers1,75514
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12190 Å2
ΔGint-62.8 kcal/mol
Surface area61480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.210, 143.560, 104.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein INTEGRIN ALPHA-IIB / GPALPHA IIB / GPIIB / PLATELET MEMBRANE GLYCOPROTEIN IIB


Mass: 49515.965 Da / Num. of mol.: 2 / Fragment: RESIDUE 32-488
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO LEC 3.2.1.8 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P08514
#2: Protein INTEGRIN BETA-3 / PLATELET MEMBRANE GLYCOPROTEIN IIIA / GPIIIA


Mass: 52087.902 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO LEC 3.2.1.8 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P05106

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Protein/peptide , 1 types, 2 molecules IJ

#5: Protein/peptide RGD PEPTIDE


Mass: 588.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)

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Antibody , 2 types, 4 molecules EHFL

#3: Antibody 10E5 FAB HEAVY CHAIN


Mass: 23766.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#4: Antibody 10E5 FAB LIGHT CHAIN


Mass: 23332.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)

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Sugars , 4 types, 4 molecules

#6: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#13: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1344 molecules

#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#12: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1318 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.35 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 8.9
Details: 11% PEG 8000, 0.2 M AMMONIUM SULFATE, 0.1 M TRIS-HCL, PH 8.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23ID / Wavelength: 0.97934
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: DOUBLE SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 146644 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 37.32 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11
Reflection shellResolution: 2.35→2.41 Å / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3T3P

3t3p


Resolution: 2.35→54.018 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2037 1017 0.7 %
Rwork0.1753 --
obs0.1755 146559 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.232 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 66.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.7988 Å20 Å20 Å2
2---0.6543 Å20 Å2
3----0.3375 Å2
Refinement stepCycle: LAST / Resolution: 2.35→54.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20079 0 248 1318 21645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621086
X-RAY DIFFRACTIONf_angle_d0.67628562
X-RAY DIFFRACTIONf_dihedral_angle_d13.9027674
X-RAY DIFFRACTIONf_chiral_restr0.0433186
X-RAY DIFFRACTIONf_plane_restr0.0033700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.47390.26971340.262920540X-RAY DIFFRACTION100
2.4739-2.62890.30571320.237920600X-RAY DIFFRACTION100
2.6289-2.83190.24791520.202720663X-RAY DIFFRACTION100
2.8319-3.11680.2381460.180420686X-RAY DIFFRACTION100
3.1168-3.56780.18341370.172220746X-RAY DIFFRACTION100
3.5678-4.49470.17451760.147620864X-RAY DIFFRACTION100
4.4947-54.0320.18131400.156721443X-RAY DIFFRACTION100
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)
10.9445-0.0788-0.33040.80070.37670.75870.00640.003-0.0049-0.0792-0.04230.08910.027-0.03780.02680.1817-0.00070.00120.0810.03870.127744.582384.466553.3158
21.37970.0142-0.24290.7833-0.28021.657-0.0774-0.0038-0.0828-0.0627-0.0183-0.13690.37240.17250.08030.26790.04490.05860.18880.01420.127378.909782.118117.8466
33.2159-1.3378-0.07990.97670.57262.4804-0.26140.0518-0.10540.22170.1098-0.60320.28660.71650.16480.49390.3152-0.07111.1278-0.10190.7299117.362883.784535.0762
41.5834-0.3256-0.67641.20671.11582.781-0.0237-0.27780.27330.11840.2052-0.23510.12480.5371-0.17690.26260.0333-0.0550.4293-0.07640.445794.9303102.168553.164
51.41210.26060.00821.94660.23840.4898-0.0025-0.13120.20940.0090.0403-0.0272-0.1390.0353-0.04160.2205-0.00370.02990.1241-0.01010.165360.9882112.277963.8442
64.48590.32210.01681.6869-0.04444.4313-0.01380.0963-0.13980.05070.3954-0.47730.45020.1813-0.21960.56230.24460.01240.94020.12520.5506109.948783.673819.2078
71.0868-0.21370.56050.7135-0.21281.933-0.12670.16730.2417-0.07460.05250.0701-0.0036-0.59320.03330.2455-0.04750.02720.41850.03750.086854.683297.255499.6057
81.05090.11250.01090.9505-0.55720.3319-0.3051-0.1019-0.22340.2018-0.1310.17360.41570.05480.34450.76020.14510.18611.27910.31921.128617.914895.7194115.825
90.8651-0.093-0.66440.05050.22021.21990.03390.497-0.0376-0.4988-0.3409-0.28860.77820.51760.3840.73960.31610.32491.09170.26650.6136110.505486.753987.0947
100.6396-0.58960.46611.17260.19511.15990.40020.865-0.1064-0.2602-0.0664-0.7887-0.30450.0562-0.13980.41190.26360.14871.06730.20741.1558146.563580.022683.381
110.4038-0.1335-0.08840.2255-0.1830.3329-0.08470.0910.50580.0168-0.2561-0.6528-0.0210.8177-0.04170.31630.00780.05731.14110.39620.9598119.792597.5928103.2844
120.09680.1958-0.18060.80490.12311.38910.45730.09790.0678-0.8535-0.0582-0.622-0.56770.2103-0.18221.1280.27290.65091.42780.61031.6964150.080995.337682.6679
131.34090.5521-0.31350.8334-0.19711.11380.1379-0.13040.16360.1728-0.19080.0605-0.0341-0.1720.04690.1775-0.01490.03010.2531-0.07520.3269.521391.118780.7064
141.5950.83250.64310.99090.36231.46510.451-0.6521-0.11130.4501-0.2937-0.170.3705-0.2128-0.10850.3292-0.0964-0.11410.407-0.09290.3587-24.137878.015988.4692
151.28860.1319-0.09370.08050.00890.57790.04650.33420.2221-0.0929-0.04080.15750.0252-0.3849-0.03280.1713-0.0075-0.03860.4595-0.02010.4263-0.519890.374761.5357
161.3133-0.06580.22111.07090.84042.6326-0.1465-0.27290.91120.0799-0.14290.3207-0.3563-0.29410.24730.26620.002-0.09310.3919-0.28510.7221-30.24390.95680.872
173.8167-2.0311-0.60671.3652-0.746.08010.406-0.5273-0.2410.37380.02140.13990.0839-0.2747-0.15310.3614-0.0463-0.00020.35230.06240.172546.3904103.583674.0419
183.595-0.41931.80020.3928-0.97392.59840.27870.2197-0.4949-0.2563-0.0551-0.15920.57150.4495-0.12780.5698-0.02280.01880.41560.01160.232471.014790.519891.4768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:454 OR RESID 2004:2007)
2X-RAY DIFFRACTION2CHAIN C AND (RESID 1:454 OR RESID 2004:2007)
3X-RAY DIFFRACTION3CHAIN B AND RESID 1:56
4X-RAY DIFFRACTION4CHAIN B AND (RESID 57:108 OR RESID 354:433)
5X-RAY DIFFRACTION5CHAIN B AND (RESID 109:352 OR RESID 2001:2003)
6X-RAY DIFFRACTION6CHAIN B AND RESID 434:471
7X-RAY DIFFRACTION7CHAIN D AND (RESID 109:352 OR RESID 2001:2003)
8X-RAY DIFFRACTION8CHAIN D AND (RESID 57:108 OR RESID 353:433)
9X-RAY DIFFRACTION9CHAIN H AND RESID 1:119
10X-RAY DIFFRACTION10CHAIN H AND RESID 120:221
11X-RAY DIFFRACTION11CHAIN L AND RESID 1:108
12X-RAY DIFFRACTION12CHAIN L AND RESID 109:214
13X-RAY DIFFRACTION13CHAIN E AND RESID 1:119
14X-RAY DIFFRACTION14CHAIN E AND RESID 120:221
15X-RAY DIFFRACTION15CHAIN F AND RESID 1:108
16X-RAY DIFFRACTION16CHAIN F AND RESID 109:214
17X-RAY DIFFRACTION17CHAIN I
18X-RAY DIFFRACTION18CHAIN J

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