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- PDB-2x1x: CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH DOMAINS 2 AND 3 OF VE... -

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Basic information

Entry
Database: PDB / ID: 2x1x
TitleCRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH DOMAINS 2 AND 3 OF VEGFR2 IN A TETRAGONAL CRYSTAL FORM
Components(VASCULAR ENDOTHELIAL GROWTH FACTOR ...) x 2
KeywordsHORMONE/SIGNALING PROTEIN / HORMONE-SIGNALING PROTEIN COMPLEX / ANGIOGENESIS / GLYCOPROTEIN / HOST-VIRUS INTERACTION / RECEPTOR / LYMPHANGIOGENESIS / IMMUNOGLOBULIN DOMAIN / DEVELOPMENTAL PROTEIN / MITOGEN
Function / homology
Function and homology information


vascular endothelial growth factor receptor 3 binding / substrate-dependent cell migration / positive regulation of lymphangiogenesis / blood vessel endothelial cell differentiation / VEGF ligand-receptor interactions / cellular response to hydrogen sulfide / positive regulation of mast cell chemotaxis / regulation of bone development / morphogenesis of embryonic epithelium / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB ...vascular endothelial growth factor receptor 3 binding / substrate-dependent cell migration / positive regulation of lymphangiogenesis / blood vessel endothelial cell differentiation / VEGF ligand-receptor interactions / cellular response to hydrogen sulfide / positive regulation of mast cell chemotaxis / regulation of bone development / morphogenesis of embryonic epithelium / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of mesenchymal stem cell proliferation / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / vascular endothelial growth factor receptor-2 signaling pathway / endothelium development / VEGF binds to VEGFR leading to receptor dimerization / endocardium development / vascular wound healing / regulation of hematopoietic progenitor cell differentiation / post-embryonic camera-type eye morphogenesis / lymph vessel development / positive regulation of vasculogenesis / mesenchymal cell proliferation / endothelial cell differentiation / induction of positive chemotaxis / positive regulation of BMP signaling pathway / surfactant homeostasis / cell migration involved in sprouting angiogenesis / epithelial cell maturation / positive regulation of positive chemotaxis / sprouting angiogenesis / embryonic hemopoiesis / positive regulation of endothelial cell chemotaxis / anchoring junction / vascular endothelial growth factor signaling pathway / positive regulation of mesenchymal cell proliferation / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of mitochondrial fission / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / lung alveolus development / positive regulation of mitochondrial depolarization / positive regulation of stem cell proliferation / growth factor binding / chemoattractant activity / : / sorting endosome / positive regulation of macroautophagy / semaphorin-plexin signaling pathway / regulation of MAPK cascade / positive regulation of cell division / cellular response to vascular endothelial growth factor stimulus / positive regulation of focal adhesion assembly / positive regulation of blood vessel endothelial cell migration / cell fate commitment / negative regulation of osteoblast differentiation / Integrin cell surface interactions / vascular endothelial growth factor receptor signaling pathway / glial cell proliferation / vasculogenesis / negative regulation of endothelial cell apoptotic process / peptidyl-tyrosine autophosphorylation / calcium ion homeostasis / coreceptor activity / ovarian follicle development / negative regulation of blood pressure / positive regulation of glial cell proliferation / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / cellular response to leukemia inhibitory factor / positive regulation of epithelial cell proliferation / platelet alpha granule lumen / VEGFR2 mediated cell proliferation / epithelial cell proliferation / stem cell proliferation / animal organ morphogenesis / positive regulation of protein secretion / Hsp90 protein binding / growth factor activity / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / GPI-linked ephrin receptor activity / transmembrane-ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / VEGFA-VEGFR2 Pathway
Similarity search - Function
CXCXC repeat / CXCXC repeat / Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / : / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain ...CXCXC repeat / CXCXC repeat / Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / : / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain / VEGFR-1-like, immunoglobulin-like domain / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Immunoglobulin domain / Cystine-knot cytokine / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like 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 / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Vascular endothelial growth factor receptor 2 / Vascular endothelial growth factor C
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLeppanen, V.-M. / Prota, A.E. / Jeltsch, M. / Anisimov, A. / Kalkkinen, N. / Strandin, T. / Lankinen, H. / Goldman, A. / Ballmer-Hofer, K. / Alitalo, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Determinants of Growth Factor Binding and Specificity by Vegf Receptor 2.
Authors: Leppanen, V.-M. / Prota, A.E. / Jeltsch, M. / Anisimov, A. / Kalkkinen, N. / Strandin, T. / Lankinen, H. / Goldman, A. / Ballmer-Hofer, K. / Alitalo, K.
History
DepositionJan 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 12, 2017Group: Advisory / Derived calculations
Category: database_PDB_caveat / struct_site / struct_site_gen
Item: _struct_site.details / _struct_site.pdbx_auth_asym_id ..._struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / struct_asym / struct_conn / 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 / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: VASCULAR ENDOTHELIAL GROWTH FACTOR C
R: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7438
Polymers36,2992
Non-polymers2,4446
Water21612
1
E: VASCULAR ENDOTHELIAL GROWTH FACTOR C
R: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
hetero molecules

E: VASCULAR ENDOTHELIAL GROWTH FACTOR C
R: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,48616
Polymers72,5994
Non-polymers4,88712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area12900 Å2
ΔGint-42.3 kcal/mol
Surface area33300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.733, 88.733, 105.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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VASCULAR ENDOTHELIAL GROWTH FACTOR ... , 2 types, 2 molecules ER

#1: Protein VASCULAR ENDOTHELIAL GROWTH FACTOR C / VEGF-C / VASCULAR ENDOTHELIAL GROWTH FACTOR-RELATED PROTEIN / VRP / FLT4 LIGAND / FLT4-L


Mass: 12390.194 Da / Num. of mol.: 1 / Fragment: VEGF HOMOLOGY DOMAIN, RESIDUES 112-215 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P49767
#2: Protein VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 / VEGF RECEPTOR 2 / VEGFR-2 / KINASE INSERT DOMAIN RECEPTOR / PROTEIN-TYROSINE KINASE RECEPTOR FLK-1


Mass: 23909.270 Da / Num. of mol.: 1 / Fragment: IG-LIKE DOMAINS 2 AND 3, RESIDUES 120-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P35968

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Sugars , 3 types, 5 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: 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.: 2
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
#6: 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 , 2 types, 13 molecules

#5: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN E, CYS 137 TO ALA
Has protein modificationY
Sequence detailsTHE VEGF-C PROTEIN STUDIED COVERS RESIDUES 112-215 WITH A C- TERMINAL 6HIS-TAG AND A C137A MUTATION. ...THE VEGF-C PROTEIN STUDIED COVERS RESIDUES 112-215 WITH A C- TERMINAL 6HIS-TAG AND A C137A MUTATION. THE VEGFR-2 PROTEIN STUDIED COVERS RESIDUES 120-326 WITH THE ARTIFICIAL RESIDUES DPIEGR AT THE C-TERMINUS.

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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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 4.6
Details: 100 MM NA-ACETATE BUFFER, PH 4.4-4.8, 50 MM CSCL, 28-32 % (W/V) JEFFAMINE 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→37 Å / Num. obs: 8092 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 17.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 29.2
Reflection shellResolution: 3.1→3.2 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 7.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X1W

2x1w


Resolution: 3.1→37 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.811 / SU B: 27.174 / SU ML: 0.49 / Cross valid method: THROUGHOUT / ESU R Free: 0.627 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES E112, R120-R121, R128-R129 AND R206-R207 ARE DISORDERED. RESIDUES Y114 AND E117 IN CHAIN E AND RESIDUES R122, S130, D131, K144, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES E112, R120-R121, R128-R129 AND R206-R207 ARE DISORDERED. RESIDUES Y114 AND E117 IN CHAIN E AND RESIDUES R122, S130, D131, K144, K266, Q268 AND H269 IN CHAIN R HAD POOR SIDECHAIN DENSITY AND WERE MODELED AS ALANINES.
RfactorNum. reflection% reflectionSelection details
Rfree0.33391 809 10 %RANDOM
Rwork0.26625 ---
obs0.27292 7273 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.667 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2--1.33 Å20 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 3.1→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 149 12 2488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222532
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1142.023443
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8655300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22423.80492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84515403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.81512
X-RAY DIFFRACTIONr_chiral_restr0.0650.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211796
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_it0.8071.51510
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50322448
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.59331022
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8514.5995
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 59 -
Rwork0.307 524 -
obs--100 %

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