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- PDB-4lxs: Structure of the Toll - Spatzle complex, a molecular hub in Droso... -

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Basic information

Entry
Database: PDB / ID: 4lxs
TitleStructure of the Toll - Spatzle complex, a molecular hub in Drosophila development and innate immunity (glycosylated form)
Components
  • Protein spaetzle C-106
  • Protein toll
KeywordsIMMUNE SYSTEM/CYTOKINE / TLR / LEUCINE-RICH REPEAT / IMMUNE SYSTEM / CYTOKINE RECEPTOR / EMBRYONIC DEVELOPMENT / INNATE IMMUNITY / RECEPTOR-LIGAND COMPLEX / IMMUNE SYSTEM-CYTOKINE complex
Function / homology
Function and homology information


positive regulation of antimicrobial peptide biosynthetic process / positive regulation of antifungal peptide biosynthetic process / positive regulation of hemocyte proliferation / regulation of embryonic pattern specification / Toll Like Receptor 10 (TLR10) Cascade / defense response to oomycetes / response to tumor cell / Formation of the trans-membrane 'signalling complex' / Adaptor protein complex binds to TL receptor at the plasma membrane / synaptic target inhibition ...positive regulation of antimicrobial peptide biosynthetic process / positive regulation of antifungal peptide biosynthetic process / positive regulation of hemocyte proliferation / regulation of embryonic pattern specification / Toll Like Receptor 10 (TLR10) Cascade / defense response to oomycetes / response to tumor cell / Formation of the trans-membrane 'signalling complex' / Adaptor protein complex binds to TL receptor at the plasma membrane / synaptic target inhibition / DL and DIF homodimers bind to TUB and phosphorylated PLL in the TL receptor 'signalling complex' / DL and DIF homodimers complexed with CACT are all phosphorylated in the TL receptor 'signalling complex' / Activated PLL kinase is autophosphorylated in the TL receptor 'signalling complex' / Phosphorylated CACT, DL and DIF homodimers dissociate from the TL receptor 'signalling complex' / PLL kinase binds to TUB in the TL receptor 'signalling complex' / positive regulation of antifungal peptide production / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / Toll binding / central nervous system formation / TIR domain binding / oocyte dorsal/ventral axis specification / cell competition in a multicellular organism / larval somatic muscle development / positive regulation of antimicrobial peptide production / antifungal innate immune response / Neutrophil degranulation / dorsal/ventral axis specification / Toll signaling pathway / detection of virus / NAD+ nucleotidase, cyclic ADP-ribose generating / dorsal/ventral pattern formation / motor neuron axon guidance / virion binding / cytokine receptor activity / negative regulation of multicellular organism growth / cytokine binding / cleavage furrow / defense response to fungus / synapse assembly / negative regulation of insulin receptor signaling pathway / cytokine activity / growth factor activity / response to hydrogen peroxide / negative regulation of cell growth / response to wounding / transmembrane signaling receptor activity / signaling receptor activity / heart development / defense response to Gram-negative bacterium / killing of cells of another organism / negative regulation of neuron apoptotic process / early endosome / receptor ligand activity / cell adhesion / defense response to Gram-positive bacterium / external side of plasma membrane / innate immune response / positive regulation of gene expression / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Spaetzle / Spaetzle / Leucine rich repeat C-terminal domain / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Toll-like receptor / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain ...Spaetzle / Spaetzle / Leucine rich repeat C-terminal domain / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Toll-like receptor / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Cystine-knot cytokine / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Ribbon / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein toll / Protein spaetzle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / MAD / Resolution: 3.3 Å
AuthorsStelter, M. / Parthier, C. / Breithaupt, C. / Stubbs, M.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of the Toll-Spatzle complex, a molecular hub in Drosophila development and innate immunity.
Authors: Parthier, C. / Stelter, M. / Ursel, C. / Fandrich, U. / Lilie, H. / Breithaupt, C. / Stubbs, M.T.
History
DepositionJul 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein toll
J: Protein spaetzle C-106
K: Protein spaetzle C-106
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,60916
Polymers115,6463
Non-polymers4,96413
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12390 Å2
ΔGint61 kcal/mol
Surface area41520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.278, 76.824, 123.822
Angle α, β, γ (deg.)90.00, 126.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 3 molecules AJK

#1: Protein Protein toll


Mass: 89632.398 Da / Num. of mol.: 1 / Fragment: UNP residues 28-802
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Tl, CG5490 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 / References: UniProt: P08953
#2: Protein Protein spaetzle C-106


Mass: 13006.618 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: spz, CG6134 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P48607

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Sugars , 4 types, 12 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-beta-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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-2-3/a4-b1_b4-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(3+1)][a-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.: 5
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
#5: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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.: 5
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 , 1 types, 1 molecules

#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM

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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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, 5% (v/v) propan-2-ol, 10% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2012
RadiationMonochromator: BESSY BL 14.2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionNumber: 43793 / Rmerge(I) obs: 0.15 / D res high: 3.91 Å / Num. obs: 22848 / % possible obs: 93.8
ReflectionResolution: 3.3→34 Å / Num. all: 19867 / Num. obs: 18492 / % possible obs: 93.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3
Reflection shellResolution: 3.3→3.4 Å / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 1.8 / % possible all: 80.3

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 3.04 Å / D res low: 46.15 Å / FOM acentric: 0.277 / FOM centric: 0.204 / Reflection acentric: 24647 / Reflection centric: 1406
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_13.0446.150011103774
ISO_23.0446.150.6670.6811082750
ISO_33.0446.151.2451.23611065748
ISO_43.0446.151.5821.48611047744
ANO_13.0446.151.0460104740
ANO_23.0446.150.9260151470
ANO_33.0446.150.6870199880
ANO_43.0446.150.3450237770
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_113.07-46.150021941
ISO_19.43-13.070049061
ISO_17.75-9.430064165
ISO_16.74-7.750075765
ISO_16.04-6.740087667
ISO_15.52-6.040097466
ISO_15.12-5.5200106367
ISO_14.79-5.1200110373
ISO_14.52-4.7900119470
ISO_14.29-4.5200124673
ISO_14.09-4.2900133269
ISO_13.92-4.0900120657
ISO_13.77-3.920020
ISO_13.63-3.770000
ISO_13.51-3.630000
ISO_13.4-3.510000
ISO_13.3-3.40000
ISO_13.2-3.30000
ISO_13.12-3.20000
ISO_13.04-3.120000
ANO_113.07-46.153.06101950
ANO_19.43-13.073.26804440
ANO_17.75-9.432.71205930
ANO_16.74-7.751.92307130
ANO_16.04-6.741.39808260
ANO_15.52-6.041.12409180
ANO_15.12-5.520.903010080
ANO_14.79-5.120.741010480
ANO_14.52-4.790.607011380
ANO_14.29-4.520.485011920
ANO_14.09-4.290.389012670
ANO_13.92-4.090.285011320
ANO_13.77-3.920000
ANO_13.63-3.770000
ANO_13.51-3.630000
ANO_13.4-3.510000
ANO_13.3-3.40000
ANO_13.2-3.30000
ANO_13.12-3.20000
ANO_13.04-3.120000
ISO_213.07-46.151.5461.32921436
ISO_29.43-13.071.6381.17148758
ISO_27.75-9.431.541.1264061
ISO_26.74-7.751.2460.88375764
ISO_26.04-6.740.9980.76187665
ISO_25.52-6.040.7910.57397462
ISO_25.12-5.520.6730.517106166
ISO_24.79-5.120.5620.407110273
ISO_24.52-4.790.4310.373119270
ISO_24.29-4.520.3420.288124472
ISO_24.09-4.290.2590.201133268
ISO_23.92-4.090.2050.191120255
ISO_23.77-3.920.158010
ISO_23.63-3.770000
ISO_23.51-3.630000
ISO_23.4-3.510000
ISO_23.3-3.40000
ISO_23.2-3.30000
ISO_23.12-3.20000
ISO_23.04-3.120000
ANO_213.07-46.154.02201960
ANO_29.43-13.074.36304650
ANO_27.75-9.433.57606220
ANO_26.74-7.752.61807330
ANO_26.04-6.741.9408530
ANO_25.52-6.041.46909460
ANO_25.12-5.521.123010280
ANO_24.79-5.120.927010890
ANO_24.52-4.790.744011700
ANO_24.29-4.520.545012300
ANO_24.09-4.290.414012920
ANO_23.92-4.090.305013410
ANO_23.77-3.920.222014410
ANO_23.63-3.770.172015100
ANO_23.51-3.630.15012310
ANO_23.4-3.510000
ANO_23.3-3.40000
ANO_23.2-3.30000
ANO_23.12-3.20000
ANO_23.04-3.120000
ISO_313.07-46.152.5692.15821537
ISO_39.43-13.072.2561.80648360
ISO_37.75-9.432.4731.89163862
ISO_36.74-7.752.1941.58175661
ISO_36.04-6.741.8551.38887466
ISO_35.52-6.041.5151.0497363
ISO_35.12-5.521.1790.804106366
ISO_34.79-5.120.9180.669110070
ISO_34.52-4.790.7340.591119169
ISO_34.29-4.520.6130.538124371
ISO_34.09-4.290.5130.386132767
ISO_33.92-4.090.4120.324120156
ISO_33.77-3.920.328010
ISO_33.63-3.770000
ISO_33.51-3.630000
ISO_33.4-3.510000
ISO_33.3-3.40000
ISO_33.2-3.30000
ISO_33.12-3.20000
ISO_33.04-3.120000
ANO_313.07-46.152.72302040
ANO_39.43-13.072.82304570
ANO_37.75-9.432.93606140
ANO_36.74-7.752.28207280
ANO_36.04-6.741.72108400
ANO_35.52-6.041.31509480
ANO_35.12-5.521.109010420
ANO_34.79-5.120.875010880
ANO_34.52-4.790.708011700
ANO_34.29-4.520.531012220
ANO_34.09-4.290.411013050
ANO_33.92-4.090.313013330
ANO_33.77-3.920.231014340
ANO_33.63-3.770.177015080
ANO_33.51-3.630.142015290
ANO_33.4-3.510.103015620
ANO_33.3-3.40.089016430
ANO_33.2-3.30.075013610
ANO_33.12-3.20000
ANO_33.04-3.120000
ISO_413.07-46.153.1182.60621339
ISO_49.43-13.072.6541.8648560
ISO_47.75-9.432.4851.97363863
ISO_46.74-7.752.2531.61275462
ISO_46.04-6.741.9331.51787364
ISO_45.52-6.041.5621.11296964
ISO_45.12-5.521.2490.913105763
ISO_44.79-5.120.9250.655109871
ISO_44.52-4.790.7450.651119070
ISO_44.29-4.520.6540.613124272
ISO_44.09-4.290.5840.43132663
ISO_43.92-4.090.4810.364120053
ISO_43.77-3.920.48020
ISO_43.63-3.770000
ISO_43.51-3.630000
ISO_43.4-3.510000
ISO_43.3-3.40000
ISO_43.2-3.30000
ISO_43.12-3.20000
ISO_43.04-3.120000
ANO_413.07-46.151.65601880
ANO_49.43-13.072.02804560
ANO_47.75-9.432.03706070
ANO_46.74-7.751.55807240
ANO_46.04-6.741.16708280
ANO_45.52-6.040.93309100
ANO_45.12-5.520.726010150
ANO_44.79-5.120.585010560
ANO_44.52-4.790.456011500
ANO_44.29-4.520.339011960
ANO_44.09-4.290.249012900
ANO_43.92-4.090.199013240
ANO_43.77-3.920.131014420
ANO_43.63-3.770.105015060
ANO_43.51-3.630.076015310
ANO_43.4-3.510.06015870
ANO_43.3-3.40.052016740
ANO_43.2-3.30.041017590
ANO_43.12-3.20.035017470
ANO_43.04-3.120.029017870
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1150.90829.2418.435SM111.541.08
2166.84564.4728.396SM130.650.92
3193.37982.1169.079SM134.611.08
4167.2568.10545.159SM202.411.07
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
13.07-46.150.8730.6922542
9.43-13.070.8360.54349069
7.75-9.430.8190.57864468
6.74-7.750.7730.52875867
6.04-6.740.7120.42787870
5.52-6.040.6550.34997571
5.12-5.520.5790.266106568
4.79-5.120.4970.201110973
4.52-4.790.440.167120371
4.29-4.520.3680.151125574
4.09-4.290.3020.098133470
3.92-4.090.2550.103137474
3.77-3.920.1760.067148575
3.63-3.770.1410.07155673
3.51-3.630.0990.046158377
3.4-3.510.0640.032162071
3.3-3.40.0520.031170872
3.2-3.30.0340.029178771
3.12-3.20.0150.006177975
3.04-3.120.0130.005181975

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHARPphasing
SOLOMONphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LXR

4lxr


Resolution: 3.3→33.948 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.49 / σ(F): 1.36 / Phase error: 31.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 925 5.01 %
Rwork0.2066 --
obs0.2094 18480 93.59 %
all-18492 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.8766 Å2
Refinement stepCycle: LAST / Resolution: 3.3→33.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6986 0 325 0 7311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057480
X-RAY DIFFRACTIONf_angle_d0.94710140
X-RAY DIFFRACTIONf_dihedral_angle_d21.2992848
X-RAY DIFFRACTIONf_chiral_restr0.061213
X-RAY DIFFRACTIONf_plane_restr0.0041277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.47390.39061170.30382205X-RAY DIFFRACTION82
3.4739-3.69130.32821230.24742329X-RAY DIFFRACTION89
3.6913-3.97590.24281310.20642508X-RAY DIFFRACTION94
3.9759-4.37520.24671360.17962588X-RAY DIFFRACTION97
4.3752-5.00660.23391380.16592620X-RAY DIFFRACTION98
5.0066-6.30120.25121390.22352646X-RAY DIFFRACTION98
6.3012-33.94940.25691410.20142659X-RAY DIFFRACTION97

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