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- PDB-3k6s: Structure of integrin alphaXbeta2 ectodomain -

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Basic information

Entry
Database: PDB / ID: 3k6s
TitleStructure of integrin alphaXbeta2 ectodomain
Components
  • Integrin alpha-X
  • Integrin beta-2
KeywordsCELL ADHESION / integrin / cell receptor / adhesion molecule / Pyrrolidone carboxylic acid
Function / homology
Function and homology information


positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / positive regulation of myelination / complement component C3b binding / neutrophil migration ...positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / positive regulation of myelination / complement component C3b binding / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / heterotypic cell-cell adhesion / integrin complex / positive regulation of leukocyte adhesion to vascular endothelial cell / cell adhesion mediated by integrin / phagocytosis, engulfment / leukocyte cell-cell adhesion / receptor clustering / amyloid-beta clearance / endodermal cell differentiation / plasma membrane raft / tertiary granule membrane / ficolin-1-rich granule membrane / cellular response to low-density lipoprotein particle stimulus / positive regulation of protein targeting to membrane / ECM proteoglycans / Integrin cell surface interactions / specific granule membrane / regulation of peptidyl-tyrosine phosphorylation / heat shock protein binding / receptor-mediated endocytosis / cell adhesion molecule binding / cell-matrix adhesion / neutrophil chemotaxis / secretory granule membrane / positive regulation of superoxide anion generation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / animal organ morphogenesis / receptor internalization / cell-cell adhesion / receptor tyrosine kinase binding / positive regulation of angiogenesis / extracellular vesicle / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell-cell signaling / signaling receptor activity / amyloid-beta binding / regulation of cell shape / defense response to virus / Interleukin-4 and Interleukin-13 signaling / receptor complex / cell adhesion / positive regulation of cell migration / inflammatory response / external side of plasma membrane / focal adhesion / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / protein kinase binding / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Tie2 ligand-binding domain fold / Tie2 ligand-binding domain superfamily / ntegrin, alpha v. Chain A, domain 4 / Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Integrin domains. Chain A, domain 2 / ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal ...Tie2 ligand-binding domain fold / Tie2 ligand-binding domain superfamily / ntegrin, alpha v. Chain A, domain 4 / Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Integrin domains. Chain A, domain 2 / ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / 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) / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / 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 / von Willebrand factor type A domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Laminin / Laminin / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / 7 Propeller / Methylamine Dehydrogenase; Chain H / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Beta Complex / Ribbon / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Integrin beta-2 / Integrin alpha-X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.5 Å
AuthorsXie, C. / Zhu, J. / Chen, X. / Mi, L. / Nishida, N. / Springer, T.A.
CitationJournal: Embo J. / Year: 2010
Title: Structure of an integrin with an alphaI domain, complement receptor type 4.
Authors: Xie, C. / Zhu, J. / Chen, X. / Mi, L. / Nishida, N. / Springer, T.A.
History
DepositionOct 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 13, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 1.3Jun 20, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-X
B: Integrin beta-2
C: Integrin alpha-X
D: Integrin beta-2
E: Integrin alpha-X
F: Integrin beta-2
G: Integrin alpha-X
H: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)796,00950
Polymers786,6058
Non-polymers9,40442
Water543
1
A: Integrin alpha-X
B: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,43914
Polymers196,6512
Non-polymers2,78812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-24 kcal/mol
Surface area83870 Å2
MethodPISA
2
C: Integrin alpha-X
D: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,74812
Polymers196,6512
Non-polymers2,09710
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-24 kcal/mol
Surface area74020 Å2
MethodPISA
3
E: Integrin alpha-X
F: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,91012
Polymers196,6512
Non-polymers2,25910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-26 kcal/mol
Surface area75370 Å2
MethodPISA
4
G: Integrin alpha-X
H: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,91012
Polymers196,6512
Non-polymers2,25910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-26 kcal/mol
Surface area75460 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42980 Å2
ΔGint-128 kcal/mol
Surface area292170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.095, 163.561, 536.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43
14
24
34
44
15
25
35
45
16
26
36
46
17
27
37
47
18
28
38
48
19
29
39
49
110
210
310
410
111
211
311
411
112
212
312
412
113
213
313
413
114
214
314
414

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:126 or resseq 330:595 or resseq 2005-2007)
211chain C and (resseq 1:126 or resseq 330:595 or resseq 2005-2007)
311chain E and (resseq 1:126 or resseq 330:595 or resseq 2005-2007)
411chain G and (resseq 1:126 or resseq 330:595 or resseq 2005-2007)
112chain A and (resseq 600:617 or resseq 627:723 or resseq 731:750 )
212chain C and (resseq 600:617 or resseq 627:723 or resseq 731:750 )
312chain E and (resseq 600:617 or resseq 627:723 or resseq 731:750 )
412chain G and (resseq 600:617 or resseq 627:723 or resseq 731:750 )
113chain A and (resseq 760:812 or resseq 827:902 )
213chain C and (resseq 760:812 or resseq 827:902 )
313chain E and (resseq 760:812 or resseq 827:902 )
413chain G and (resseq 760:812 or resseq 827:902 )
114chain A and (resseq 903:986 or resseq 995:1081 )
214chain C and (resseq 903:986 or resseq 995:1081 )
314chain E and (resseq 903:986 or resseq 995:1081 )
414chain G and (resseq 903:986 or resseq 995:1081 )
115chain B and (resseq 1:56 )
215chain D and (resseq 1:56 )
315chain F and (resseq 1:56 )
415chain H and (resseq 1:56 )
116chain B and (resseq 60:67 or resseq 73:99 or resseq 348:423 )
216chain D and (resseq 60:67 or resseq 73:99 or resseq 348:423 )
316chain F and (resseq 60:67 or resseq 73:99 or resseq 348:423 )
416chain H and (resseq 60:67 or resseq 73:99 or resseq 348:423 )
117chain B and (resseq 436:449 or resseq 456:461 )
217chain D and (resseq 436:449 or resseq 456:461 )
317chain F and (resseq 436:449 or resseq 456:461 )
417chain H and (resseq 436:449 or resseq 456:461 )
118chain B and (resseq 102:342 or resid 2002 )
218chain D and (resseq 102:342 or resid 2002 )
318chain F and (resseq 102:342 or resid 2002 )
418chain H and (resseq 102:342 or resid 2002 )
119chain B and (resseq 463:473 )
219chain D and (resseq 463:473 )
319chain F and (resseq 463:473 )
419chain H and (resseq 463:473 )
1110chain B and (resseq 475:512 )
2110chain D and (resseq 475:512 )
3110chain F and (resseq 475:512 )
4110chain H and (resseq 475:512 )
1111chain B and (resseq 516:550 )
2111chain D and (resseq 516:550 )
3111chain F and (resseq 516:550 )
4111chain H and (resseq 516:550 )
1112chain B and (resseq 555:592 )
2112chain D and (resseq 555:592 )
3112chain F and (resseq 555:592 )
4112chain H and (resseq 555:592 )
1113chain B and (resseq 593:597 )
2113chain D and (resseq 593:597 )
3113chain F and (resseq 593:597 )
4113chain H and (resseq 593:597 )
1114chain B and (resseq 600:673 )
2114chain D and (resseq 600:673 )
3114chain F and (resseq 600:673 )
4114chain H and (resseq 600:673 )

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Integrin alpha-X / Leukocyte adhesion glycoprotein p150 / 95 alpha chain / Leukocyte adhesion receptor p150 / 95 / Leu ...Leukocyte adhesion glycoprotein p150 / 95 alpha chain / Leukocyte adhesion receptor p150 / 95 / Leu M5 / CD11 antigen-like family member C


Mass: 120708.203 Da / Num. of mol.: 4 / Fragment: residues 20-1103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD11C, ITGAX / Plasmid: pcDNA3.1(-) / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO Lec 3.2.8.1 / References: UniProt: P20702
#2: Protein
Integrin beta-2 / Cell surface adhesion glycoproteins LFA-1/CR3/p150 / 95 subunit beta / Complement receptor C3 subunit beta


Mass: 75942.992 Da / Num. of mol.: 4 / Fragment: residues 23-700
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD18, ITGB2, MFI7 / Plasmid: pEF1/puro / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO Lec 3.2.8.1 / References: UniProt: P05107

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Sugars , 5 types, 25 molecules

#3: 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.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
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 , 3 types, 20 molecules

#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 3.69 Å3/Da / Density % sol: 66.64 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6.5
Details: 0.55M tri-sodium citrate, 0.1M imidazole, pH 6.5, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97926,0.97942,0.96419
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2006
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.979421
30.964191
ReflectionResolution: 3.5→50 Å / Num. all: 147271 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.53 % / Biso Wilson estimate: 80.6 Å2 / Rmerge(I) obs: 0.161 / Rsym value: 0.161 / Net I/σ(I): 12
Reflection shellResolution: 3.5→3.61 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.371 / Mean I/σ(I) obs: 1.93 / Num. unique all: 19338 / Rsym value: 1.371 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.5→48.613 Å / SU ML: 0.8 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: MLHL / Details: MLHL refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.3347 1536 1.04 %random
Rwork0.2971 ---
all0.2975 147271 --
obs0.2975 147271 99.96 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 150 Å2 / ksol: 0.397 e/Å3
Refine analyzeLuzzati sigma a free: 0.8 Å
Refinement stepCycle: LAST / Resolution: 3.5→48.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49597 0 587 3 50187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00399973
X-RAY DIFFRACTIONf_angle_d0.648179807
X-RAY DIFFRACTIONf_dihedral_angle_d13.18925172
X-RAY DIFFRACTIONf_chiral_restr0.0487755
X-RAY DIFFRACTIONf_plane_restr0.00415838
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5796X-RAY DIFFRACTIONPOSITIONAL
12C5796X-RAY DIFFRACTIONPOSITIONAL0.008
13E5796X-RAY DIFFRACTIONPOSITIONAL0.007
14G5796X-RAY DIFFRACTIONPOSITIONAL0.008
21A2150X-RAY DIFFRACTIONPOSITIONAL
22C2150X-RAY DIFFRACTIONPOSITIONAL0.005
23E2150X-RAY DIFFRACTIONPOSITIONAL0.004
24G2150X-RAY DIFFRACTIONPOSITIONAL0.005
31A1941X-RAY DIFFRACTIONPOSITIONAL
32C1941X-RAY DIFFRACTIONPOSITIONAL0.005
33E1941X-RAY DIFFRACTIONPOSITIONAL0.005
34G1941X-RAY DIFFRACTIONPOSITIONAL0.004
41A2709X-RAY DIFFRACTIONPOSITIONAL
42C2709X-RAY DIFFRACTIONPOSITIONAL0.006
43E2709X-RAY DIFFRACTIONPOSITIONAL0.023
44G2709X-RAY DIFFRACTIONPOSITIONAL0.005
51B826X-RAY DIFFRACTIONPOSITIONAL
52D826X-RAY DIFFRACTIONPOSITIONAL0.004
53F826X-RAY DIFFRACTIONPOSITIONAL0.002
54H826X-RAY DIFFRACTIONPOSITIONAL0.003
61B1721X-RAY DIFFRACTIONPOSITIONAL
62D1721X-RAY DIFFRACTIONPOSITIONAL0.006
63F1721X-RAY DIFFRACTIONPOSITIONAL0.006
64H1721X-RAY DIFFRACTIONPOSITIONAL0.009
71B283X-RAY DIFFRACTIONPOSITIONAL
72D283X-RAY DIFFRACTIONPOSITIONAL0.015
73F283X-RAY DIFFRACTIONPOSITIONAL0.008
74H283X-RAY DIFFRACTIONPOSITIONAL0.004
81B3752X-RAY DIFFRACTIONPOSITIONAL
82D3752X-RAY DIFFRACTIONPOSITIONAL0.009
83F3752X-RAY DIFFRACTIONPOSITIONAL0.004
84H3752X-RAY DIFFRACTIONPOSITIONAL0.005
91B157X-RAY DIFFRACTIONPOSITIONAL
92D157X-RAY DIFFRACTIONPOSITIONAL0.056
93F157X-RAY DIFFRACTIONPOSITIONAL0.055
94H157X-RAY DIFFRACTIONPOSITIONAL0.053
101B536X-RAY DIFFRACTIONPOSITIONAL
102D536X-RAY DIFFRACTIONPOSITIONAL0.011
103F536X-RAY DIFFRACTIONPOSITIONAL0.004
104H536X-RAY DIFFRACTIONPOSITIONAL0.004
111B479X-RAY DIFFRACTIONPOSITIONAL
112D479X-RAY DIFFRACTIONPOSITIONAL0.004
113F479X-RAY DIFFRACTIONPOSITIONAL0.004
114H479X-RAY DIFFRACTIONPOSITIONAL0.003
121B568X-RAY DIFFRACTIONPOSITIONAL
122D568X-RAY DIFFRACTIONPOSITIONAL0.004
123F568X-RAY DIFFRACTIONPOSITIONAL0.004
124H568X-RAY DIFFRACTIONPOSITIONAL0.003
131B55X-RAY DIFFRACTIONPOSITIONAL
132D55X-RAY DIFFRACTIONPOSITIONAL0.01
133F55X-RAY DIFFRACTIONPOSITIONAL0.036
134H55X-RAY DIFFRACTIONPOSITIONAL0.02
141B1114X-RAY DIFFRACTIONPOSITIONAL
142D1114X-RAY DIFFRACTIONPOSITIONAL0.003
143F1114X-RAY DIFFRACTIONPOSITIONAL0.035
144H1114X-RAY DIFFRACTIONPOSITIONAL0.035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.61290.43811420.433513095X-RAY DIFFRACTION100
3.6129-3.7420.37781330.374813108X-RAY DIFFRACTION100
3.742-3.89180.37011300.342313180X-RAY DIFFRACTION100
3.8918-4.06880.40381320.317313059X-RAY DIFFRACTION100
4.0688-4.28320.31821410.29513193X-RAY DIFFRACTION100
4.2832-4.55140.30731540.245613148X-RAY DIFFRACTION100
4.5514-4.90250.27461510.217613184X-RAY DIFFRACTION100
4.9025-5.39530.26511350.217613232X-RAY DIFFRACTION100
5.3953-6.17470.31511280.240513319X-RAY DIFFRACTION100
6.1747-7.77430.33931550.260213433X-RAY DIFFRACTION100
7.7743-48.6180.26351350.26213784X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.0714-0.1659-0.28940.46220.28310.7779-0.20780.2931-0.0089-0.1683-0.665-0.1551-0.03790.1454-0.9279-1.9640.1416-1.3569-0.20990.2785-0.3532-49.278866.062416.3271
2-0.0656-0.036-0.19050.5144-0.00550.67180.03060.7177-0.5501-0.8706-0.35230.30710.9672-0.1025-0.69460.3277-0.1996-0.3078-1.5403-0.30130.0865
3-0.16230.0333-0.027-0.1512-0.03610.02740.0808-0.6332-0.09650.35020.239-0.27780.6922-0.66820.148-0.0024-0.6869-1.27571.3920.2505-0.3486
40.28320.0372-0.2789-0.16150.08270.196-0.3203-0.6454-0.1130.74150.06230.0920.14850.0485-0.4702-1.0917-0.32120.4590.6868-0.0399-1.0121
5-0.00570.1358-0.18172.0040.3451-0.06920.02290.42010.3701-0.9139-0.16060.5321-0.4764-0.125-0.70420.41050.0244-0.0749-0.05840.1571-0.1622
60.03630.0328-0.02090.0169-0.11990.06740.067-0.1705-0.4818-0.02980.14380.01910.32620.0769-0.0726-1.09880.1394-0.1111-1.05850.53820.075
71.16410.54530.15140.43250.23450.18220.1977-0.59830.1272-0.0627-0.0992-0.62060.1856-0.0711-0.4732-2.20390.2586-0.5688-0.4649-0.03140.1426
80.23970.2648-0.08530.3125-0.01480.0971-0.0643-0.0992-0.0311-0.0265-0.05920.696-0.1978-0.0303-1.0487-1.25090.159-0.02730.0073-0.0948-0.2341
90.20050.20030.113-0.03220.0958-0.0379-0.1104-0.13390.6112-0.0909-0.05460.2407-0.0999-0.2296-0.9612-1.7543-0.4470.4538-0.912-0.16350.0147
100.19750.2623-0.23630.0647-0.09690.151-0.0358-0.0675-0.431-0.2628-0.3592-0.05610.0050.0452-0.9803-1.8434-0.2344-0.3487-0.6160.2624-0.4084
110.46780.4826-0.13320.5037-0.19380.2641-0.2139-0.38170.27490.0002-0.0679-0.6201-0.19930.0244-0.2025-1.1893-0.2246-0.7033-1.14550.165-0.1037
120.9924-0.0626-0.55540.64620.56840.4475-0.1459-0.4983-0.23050.34190.40720.28370.40140.1304-0.1194-0.74710.1176-0.7185-0.60890.0655-0.5597
130.46890.08540.2594-0.00040.06280.22190.0767-0.07070.1317-0.1889-0.22540.0198-0.02560.2230.0411-1.5854-0.0056-0.0803-0.2672-0.5766-0.6162
14-0.03420.214-0.14490.2015-0.22650.0633-0.28080.223-0.1111-0.6479-0.035-0.35790.39850.1653-0.1783-0.617-0.70160.8837-1.39770.2512-0.7865
150.26270.045-0.01140.06390.01750.2761-0.001-0.8065-0.23440.0997-0.30820.0140.02650.2739-0.31450.3797-0.1030.01860.81260.3238-0.2217
160.1125-0.0401-0.1312-0.0330.0544-0.01110.1609-0.54150.32910.2075-0.0732-0.2293-0.20540.26640.33740.0003-0.3312-0.30051.0448-0.13820.0104
170.46010.21750.52620.32850.08540.7524-0.2039-0.2055-0.0074-0.2663-0.03410.3621-0.0201-0.3794-0.0664-0.2545-0.3511-0.6909-0.3619-0.5637-0.888
18-0.0034-0.01260.0135-0.00550.01010.00290.07570.01970.0205-0.0582-0.0883-0.00780.029-0.017701.85830.23080.1251.30090.31851.6865
190.00190.01270.01230.00780.00110.0113-0.0373-0.00180.176-0.05530.0495-0.0206-0.08680.0936-02.46590.1633-0.16241.8081-0.11262.31
20-0.0115-0.0070.00920.0030.0008-0.00130.1059-0.08640.177-0.0709-0.0073-0.0043-0.0963-0.0347-01.85760.3623-0.49951.726-0.33361.4236
210.00010.00060.0004-0.0012-0.01250.00470.11630.0045-0.0381-0.09630.02420.09350.0582-0.0109-01.891-0.0068-0.15841.6782-0.40141.7568
220.1518-0.0596-0.01240.07010.0237-0.0310.25630.2905-0.08010.1267-0.28310.02370.0836-0.0152-0.04461.770.50430.2604-0.09450.0121.1488
23-0.0137-0.00670.0094-0.0457-0.0232-0.0186-0.0326-0.0183-0.07120.19970.0723-0.06050.2065-0.0264-01.33120.5129-0.88621.78190.28912.1049
240.0443-0.0349-0.01560.3811-0.1465-0.0514-0.28990.06840.05580.37730.3221-0.0224-0.0701-0.256-0.02740.02190.35960.19731.8557-0.43610.8364
250.10420.0388-0.11150.0663-0.0439-0.00750.3927-0.0859-0.00790.0611-0.1102-0.2113-0.3572-0.09560.00231.77950.5573-0.55980.29570.01691.5224
260.0694-0.0457-0.00850.0059-0.00620.05250.01630.07920.01510.1301-0.02370.1045-0.08780.07720.01211.6370.00240.24190.24830.78711.1059
270.34350.7663-0.89610.34260.01070.25680.04060.06750.0380.1356-0.11530.16650.0942-0.17440.00370.97240.06990.1591.4419-0.05691.8354
28-0.029-0.08920.05220.15520.05910.0817-0.03640.02160.04490.0875-0.095-0.03290.03120.1504-0.0138-0.1050.187-0.6411.3774-0.25891.0652
29-0.00470.00770.00110.01360.00310.0047-0.07550.1296-0.01620.0225-0.0262-0.05820.0767-0.035401.71930.0217-0.36350.7791-0.46271.4428
30-0.0017-0.04910.03620.2020.10780.1960.0534-0.0970.1524-0.37530.1748-0.1755-0.02050.0040.22141.57440.62610.09190.2637-0.07090.0176
310.176-0.0952-0.06060.0385-0.00040.01590.2597-0.08570.0326-0.16320.2130.1179-0.37230.11330.01681.58130.0129-0.69411.41710.37460.7122
320.10230.0197-0.0734-0.00860.00180.04170.147-0.6278-0.01160.1327-0.0153-0.13350.20780.05310.00480.79020.1858-0.07921.8719-0.39470.1895
330.181-0.05310.028-0.0126-0.03420.0939-0.0901-0.0075-0.1384-0.20010.03820.11740.190.4876-0.0881.86740.4512-0.53740.47460.10250.4442
340.0137-0.01410.00650.02510.01710.0090.0844-0.0523-0.1411-0.0770.13280.00940.00280.03270.00051.5322-0.09760.0230.40460.26460.4067
350.0127-0.00120.0024-0.00640.0179-0.0115-0.0648-0.18180.09360.00020.091-0.04810.0632-0.077500.3141-0.132-0.10961.67180.16221.0396
36-0.0113-0.0067-0.0325-0.03130.0160.1078-0.0174-0.2082-0.0554-0.0320.11640.1366-0.1119-0.07150.0068-0.0607-0.2616-0.27251.4409-0.21820.4037
370.02410.02040.0796-0.0130.0028-0.00840.0766-0.02960.0353-0.22450.04590.03160.0161-0.1330.01481.3773-0.4526-0.2968-0.027-0.37460.7831
38-0.02680.0168-0.00610.0116-0.00510.03110.05750.0348-0.0403-0.00880.05570.03420.0557-0.02380.01951.2998-0.6596-0.17890.25410.18360.1617
390.01070.0032-0.0106-0.0057-0.00380.00460.14930.039-0.08630.10610.10050.0223-0.00910.093-00.6627-0.04420.30241.71810.14171.0342
400.05950.11020.0002-0.01830.02710.12930.1168-0.04330.02690.16580.0372-0.0980.0846-0.06050.1459-0.3112-0.4708-0.40751.2894-0.22240.0723
410.00240.0735-0.17430.04020.00140.2820.03110.09690.0850.07060.1801-0.0021-0.07780.05790.07020.8673-0.3583-0.1580.2662-0.18130.3978
420.0888-0.00760.0983-0.00960.02770.0287-0.10880.05950.1867-0.0603-0.1064-0.0447-0.05050.1315-0.01030.4840.18090.19170.09530.39450.6958
43-0.0022-0.0040.0034-0.00180.0051-0.00790.0672-0.00070.01630.07320.0512-0.08330.0678-0.024200.7878-0.08290.07060.88450.54471.0695
440.0033-0.0067-0.01230.00630.00140.0079-0.0983-0.01790.0150.0233-0.2088-0.02170.0410.0399-00.818-0.2704-0.03470.9243-0.56110.6998
45-0.0138-0.01240.02320.04670.04020.0102-0.16280.0748-0.0377-0.0741-0.09720.03280.0006-0.1003-0.0450.2674-0.1473-0.53810.3013-0.11070.685
460.042-0.0608-0.012-0.04710.01590.0240.154-0.07580.09060.07040.0565-0.0142-0.2656-0.24470.01570.93830.11040.26180.73220.16220.0564
470.00250.01050.018-0.0306-0.02720.01080.1070.1124-0.21990.09930.0497-0.2111-0.0466-0.1239-01.5677-0.4744-0.57051.85740.72420.9766
480.001-0.0097-0.0067-0.0319-0.00180.01970.0741-0.09130.12420.278-0.0401-0.01970.05770.0295-01.1319-0.3384-0.02561.3624-0.47280.8271
490.089-0.0029-0.0780.14630.00880.08210.1823-0.0133-0.06210.14530.0064-0.06110.08810.37560.06960.8109-0.0389-0.28460.5903-0.17570.0942
Refinement TLS groupSelection details: chain H and resseq 600-676

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