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- PDB-9s9a: Crystal structure of the BRL3 ectodomain from Arabidopsis thalian... -

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Basic information

Entry
Database: PDB / ID: 9s9a
TitleCrystal structure of the BRL3 ectodomain from Arabidopsis thaliana in complex with 6-deoxocastasterone.
ComponentsReceptor-like protein kinase BRI1-like 3
KeywordsMEMBRANE PROTEIN / receptor kinase / steroid receptor / brassinosteroids / leucine-rich repeat
Function / homology
Function and homology information


detection of brassinosteroid stimulus / brassinosteroid mediated signaling pathway / response to water deprivation / response to light stimulus / steroid binding / hormone-mediated signaling pathway / transmembrane receptor protein tyrosine kinase activity / post-embryonic development / receptor protein-tyrosine kinase / signaling receptor activity ...detection of brassinosteroid stimulus / brassinosteroid mediated signaling pathway / response to water deprivation / response to light stimulus / steroid binding / hormone-mediated signaling pathway / transmembrane receptor protein tyrosine kinase activity / post-embryonic development / receptor protein-tyrosine kinase / signaling receptor activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
: / Brassinosteroid receptor BRI1, island domain / Brassinosteroid receptor island domain / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich repeat / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...: / Brassinosteroid receptor BRI1, island domain / Brassinosteroid receptor island domain / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich repeat / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / ACETATE ION / Receptor-like protein kinase BRI1-like 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.2 Å
AuthorsCaregnato, A. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_205201 Switzerland
CitationJournal: To Be Published
Title: A mechanistic framework for the recognition of chemically diverse brassinosteroids by BRI1-family receptor kinases.
Authors: Caregnato, A. / Chen, H. / Kvasnica, M. / Hohmann, U. / Oklestkova, J. / Ferrer, K. / Broger, L. / Hothorn, L.A. / Strnad, M. / Hothorn, M.
History
DepositionAug 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 2.0Feb 18, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity_name_com / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly_auth_evidence / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_oper
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_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _chem_comp.pdbx_synonyms / _chem_comp_atom.atom_id / _chem_comp_atom.pdbx_stereo_config / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _entity_name_com.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_symm_contact.dist / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3]
Description: Chirality error
Details: Dear Curator, Matthew Conroy from LIPID MAPS has informed us that our ligand entry A1JMI (6-deoxocastasterone) contains a chirality error at position C5. We have generated new ligand ...Details: Dear Curator, Matthew Conroy from LIPID MAPS has informed us that our ligand entry A1JMI (6-deoxocastasterone) contains a chirality error at position C5. We have generated new ligand restraints and corrected the error. Best regards, Michael Hothorn
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-like protein kinase BRI1-like 3
B: Receptor-like protein kinase BRI1-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,82927
Polymers167,2392
Non-polymers11,59025
Water00
1
A: Receptor-like protein kinase BRI1-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,22313
Polymers83,6201
Non-polymers5,60312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-like protein kinase BRI1-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,60614
Polymers83,6201
Non-polymers5,98713
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.163, 82.688, 122.196
Angle α, β, γ (deg.)107.015, 91.353, 112.460
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 31 and (name N or name...
d_2ens_1(chain "B" and ((resid 31 and (name N or name...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11VALVALLYSLYSAA31 - 20431 - 204
d_12LEULEULEULEUAA206 - 224206 - 224
d_13GLUGLUASNASNAA226 - 249226 - 249
d_14LYSLYSGLUGLUAA251 - 254251 - 254
d_15LEULEUSERSERAA256 - 324256 - 324
d_16GLYGLYGLYGLYAA326 - 334326 - 334
d_17ASNASNLEULEUAA336 - 398336 - 398
d_18SERSERSERSERAA400 - 490400 - 490
d_19PROPROSERSERAA492 - 757492 - 757
d_110A1JMIA1JMIA1JMIA1JMIAQ801
d_111NAGNAGNAGNAGAR802
d_112NAGNAGNAGNAGCC1
d_113NAGNAGNAGNAGCC2
d_114NAGNAGNAGNAGAS803
d_115NAGNAGNAGNAGAT804
d_116NAGNAGNAGNAGDD1
d_117MANMANMANMANDD9
d_118MANMANMANMANDD4
d_119MANMANMANMANDD10
d_120MANMANMANMANDD7
d_121MANMANMANMANDD8
d_122MANMANMANMANDD5
d_123MANMANMANMANDD6
d_124NAGNAGNAGNAGEE1
d_125NAGNAGNAGNAGEE2
d_126NAGNAGNAGNAGFF1
d_127NAGNAGNAGNAGFF2
d_128NAGNAGNAGNAGGG1
d_129NAGNAGNAGNAGGG2
d_130NAGNAGNAGNAGHH1
d_131NAGNAGNAGNAGHH2
d_132NAGNAGNAGNAGII1
d_133NAGNAGNAGNAGII2
d_21VALVALTRPTRPBB31 - 5631 - 56
d_22ASPASPLYSLYSBB63 - 20463 - 204
d_23LEULEULEULEUBB206 - 224206 - 224
d_24GLUGLUASNASNBB226 - 249226 - 249
d_25LYSLYSGLUGLUBB251 - 254251 - 254
d_26LEULEUSERSERBB256 - 324256 - 324
d_27GLYGLYGLYGLYBB326 - 334326 - 334
d_28ASNASNLEULEUBB336 - 398336 - 398
d_29SERSERSERSERBB400 - 490400 - 490
d_210PROPROSERSERBB492 - 757492 - 757
d_211A1JMIA1JMIA1JMIA1JMIBV801
d_212NAGNAGNAGNAGBW802
d_213NAGNAGNAGNAGJJ1
d_214NAGNAGNAGNAGJJ2
d_215NAGNAGNAGNAGBX803
d_216NAGNAGNAGNAGKK1
d_217NAGNAGNAGNAGKK2
d_218MANMANMANMANKK7
d_219MANMANMANMANKK5
d_220MANMANMANMANKK6
d_221MANMANMANMANKK10
d_222MANMANMANMANKK11
d_223MANMANMANMANKK8
d_224MANMANMANMANKK9
d_225NAGNAGNAGNAGLL1
d_226NAGNAGNAGNAGLL2
d_227NAGNAGNAGNAGBY804
d_228NAGNAGNAGNAGMM1
d_229NAGNAGNAGNAGMM2
d_230NAGNAGNAGNAGNN1
d_231NAGNAGNAGNAGNN2
d_232NAGNAGNAGNAGOO1
d_233NAGNAGNAGNAGOO2
d_234NAGNAGNAGNAGBZ805

NCS oper: (Code: givenMatrix: (-0.46420162995, -0.848233013073, -0.254985494264), (-0.840347677216, 0.33080565162, 0.429398884785), (-0.279879667268, 0.413604130045, -0.866371164952)Vector: 35. ...NCS oper: (Code: given
Matrix: (-0.46420162995, -0.848233013073, -0.254985494264), (-0.840347677216, 0.33080565162, 0.429398884785), (-0.279879667268, 0.413604130045, -0.866371164952)
Vector: 35.1140714252, -7.36152187111, 96.3310392897)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Receptor-like protein kinase BRI1-like 3 / BRASSINOSTEROID INSENSITIVE 1-like protein 3 / BRL3 leucine-rich repeat ectodomain


Mass: 83619.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col-0 / Gene: BRL3, At3g13380, MRP15.1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9LJF3, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase

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Sugars , 5 types, 22 molecules

#2: 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.: 11
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
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-i1_g2-h1_i2-j1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1883.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}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-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
#7: 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.: 8 / Source method: obtained synthetically / 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, 3 molecules

#6: Chemical ChemComp-A1JMI / 6-deoxocastasterone / (2R,3S,5S,8R,9S,10S,13S,14S,17R)-17-[(2S,3R,4R,5S)-5,6-dimethyl-3,4-bis(oxidanyl)heptan-2-yl]-10,13-dimethyl-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-2,3-diol


Mass: 450.694 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C28H50O4
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2

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Details

Has ligand of interestN
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: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 23% PEG 3350, 0.2 M Li2So4, 0.1 M citric acid pH 4.0, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 3.2→48.11 Å / Num. obs: 32179 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 114.55 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.197 / Net I/σ(I): 5.5
Reflection shellResolution: 3.2→3.39 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5210 / CC1/2: 0.23 / Rrim(I) all: 3.851 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.2→48.11 Å / SU ML: 0.679 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.8244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2803 1585 5.07 %
Rwork0.2205 29653 -
obs0.2236 31238 89.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 137.8 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10832 0 770 0 11602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002211843
X-RAY DIFFRACTIONf_angle_d0.60216118
X-RAY DIFFRACTIONf_chiral_restr0.04092070
X-RAY DIFFRACTIONf_plane_restr0.00391993
X-RAY DIFFRACTIONf_dihedral_angle_d11.81084878
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 5.01881875222 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.30.48631180.4472131X-RAY DIFFRACTION69.48
3.3-3.420.45741470.38092673X-RAY DIFFRACTION89.16
3.42-3.560.40581520.33152782X-RAY DIFFRACTION92.44
3.56-3.720.37311450.29572739X-RAY DIFFRACTION91.18
3.72-3.920.36251450.26972736X-RAY DIFFRACTION89.53
3.92-4.160.29931340.20242394X-RAY DIFFRACTION79.4
4.16-4.480.24791450.18422829X-RAY DIFFRACTION93.85
4.48-4.930.25791540.17482897X-RAY DIFFRACTION96.28
4.93-5.650.25471550.19542880X-RAY DIFFRACTION95.11
5.65-7.110.2911400.23992815X-RAY DIFFRACTION93.07
7.11-48.110.2251500.18652777X-RAY DIFFRACTION91.7
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)
11.905085378580.107965938827-1.04785773680.154350204393-0.8745977162015.19750134572-0.205193999409-0.5142670476190.07342563712280.37322002312-0.2982560621520.4140694864891.88330205185-0.9747987872710.4527737294881.64249405117-0.2894622119320.1447521770121.56009304730.03577137599360.978148954014-30.0825149839-14.127869722994.5119383522
23.378661934670.578066425434-0.2291565139625.734898616910.7610177422072.76515421535-0.24644729608-0.337281557961-0.2731643695790.892358430437-0.240921536323-0.09201676483660.88346820.4425450632730.4244212993931.260102954710.1696385924890.1503272965581.203769794790.2616922353360.985845730505-11.0281355872-6.2063245793886.5558636287
32.04529460778-1.70856105831-1.532091483611.582547733121.190070084751.181344082260.3509467630480.2478238801580.0334596289868-0.51162429934-0.33012345058-0.164401919804-0.214282856313-0.454254481258-0.007405058520810.9946488449130.306999456698-0.009061445324921.207221709920.1925393065730.824108957603-20.991406045926.167514843971.5429377658
47.13696112982-3.0957062115-4.410395039122.503899970550.8686217539387.476635420190.781996933941-0.02101409854590.566182177626-0.176686726234-0.0764207642032-0.297484165297-2.01906543356-0.199471314178-0.6738385269041.319408730640.10378012302-0.05581515335671.007274826650.09484547226580.821026077191-24.147036911938.246138256692.0041509169
51.74500757306-0.00777515021430.4147423681151.99051047221.414521662173.762670892870.0963808855099-0.0645273497474-0.08495029980050.32121644986-0.358512077871-0.200027125378-0.2381218532280.3423007928540.2433015775781.01801226230.2269907832510.1464586007731.267977253830.2833206379940.88301197564-24.976040778739.4402819109109.660200596
65.22366091754-2.84068283087-0.6961514274196.92743525051-0.591967392654.227801116550.1366323949521.235757444730.0214050935256-0.779312448076-0.283316043116-0.8730810624110.04753732299610.02517110279460.1431399928431.46124192005-0.1244891537140.1203417951231.31900193040.02077724282111.0351441461535.772087336849.594483763215.6003353852
70.791704486466-1.17345524565-0.3936979414163.619632565850.3834436201711.18957936792-0.387885633653-0.110307237087-0.110557363490.5501864330430.10730625811-0.08726708468840.2612813866940.121399627950.2466074326950.836578917227-0.0512189866633-0.04686761919970.8877440810970.03756715996530.64400697647.8765130206646.368619721145.0779727411
81.66882363282-1.549691489791.104168849897.45670448805-1.395402001232.8788339305-0.04726428021550.1602775081110.145308250135-0.02734984789370.4065905110820.487215401612-0.424714586712-0.678088766184-0.2529071302681.036160448030.03469976856440.03709613635081.126353145360.180956900680.855419720368-8.502550481666.452190701936.9995781734
92.624262780690.5783947457241.498544147234.007020490150.5909627773464.14290249867-0.1072376776640.2467792640610.109928130862-0.980477926033-0.00333543107035-0.0681412275094-0.754007318549-0.760486182757-0.002491340028561.405733663380.153595547550.09993991766971.075055796230.2149166814310.853902193035-17.830066007475.760632295621.7617828744
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 31 through 87 )AA31 - 871 - 51
22chain 'A' and (resid 88 through 219 )AA88 - 21952 - 183
33chain 'A' and (resid 220 through 553 )AA220 - 553184 - 517
44chain 'A' and (resid 554 through 623 )AA554 - 623518 - 587
55chain 'A' and (resid 624 through 757 )AA624 - 757588 - 721
66chain 'B' and (resid 31 through 127 )BB31 - 1271 - 97
77chain 'B' and (resid 128 through 553 )BB128 - 55398 - 523
88chain 'B' and (resid 554 through 656 )BB554 - 656524 - 626
99chain 'B' and (resid 657 through 757 )BB657 - 757627 - 727

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