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- PDB-3wwq: Crystal structure of FAAP20 UBZ domain in complex with Lys63-link... -

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Basic information

Entry
Database: PDB / ID: 3wwq
TitleCrystal structure of FAAP20 UBZ domain in complex with Lys63-linked diubiquitin
Components
  • (Ubiquitin) x 2
  • Fanconi anemia-associated protein of 20 kDa
KeywordsPROTEIN BINDING/METAL BINDING PROTEIN / protein complex / DNA repair / PROTEIN BINDING-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex / Negative regulation of FLT3 / Downregulation of SMAD2/3:SMAD4 transcriptional activity ...APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex / Negative regulation of FLT3 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of expression of SLITs and ROBOs / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Alpha-protein kinase 1 signaling pathway / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / Regulation of NF-kappa B signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of BACH1 activity / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / Regulation of innate immune responses to cytosolic DNA / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / PINK1-PRKN Mediated Mitophagy / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Termination of translesion DNA synthesis / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Inactivation of CSF3 (G-CSF) signaling / Senescence-Associated Secretory Phenotype (SASP) / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR1-induced NF-kappa-B signaling pathway / Josephin domain DUBs / Dual Incision in GG-NER / Regulation of FZD by ubiquitination / Downregulation of ERBB2 signaling / Dual incision in TC-NER / IKK complex recruitment mediated by RIP1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Oncogene Induced Senescence / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Metalloprotease DUBs / Gap-filling DNA repair synthesis and ligation in TC-NER / Degradation of AXIN / Regulation of TNFR1 signaling / EGFR downregulation / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / G2/M Checkpoints / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity / Deactivation of the beta-catenin transactivating complex / Regulation of RAS by GAPs / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / Ovarian tumor domain proteases / RAS processing / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Cyclin D associated events in G1
Similarity search - Function
FAAP20, zinc finger UBZ2-type / FAAP20, FANCA interaction domain / Ubiquitin-binding zinc-finger / FAAP20 FANCA interaction domain / Zinc finger UBZ2-type profile. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues ...FAAP20, zinc finger UBZ2-type / FAAP20, FANCA interaction domain / Ubiquitin-binding zinc-finger / FAAP20 FANCA interaction domain / Zinc finger UBZ2-type profile. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / Fanconi anemia core complex-associated protein 20
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSato, Y. / Fukai, S.
CitationJournal: Plos One / Year: 2015
Title: Structural Basis for Ubiquitin Recognition by Ubiquitin-Binding Zinc Finger of FAAP20
Authors: Toma, A. / Takahashi, T.S. / Sato, Y. / Yamagata, A. / Goto-Ito, S. / Nakada, S. / Fukuto, A. / Horikoshi, Y. / Tashiro, S. / Fukai, S.
History
DepositionJun 23, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: Fanconi anemia-associated protein of 20 kDa
D: Ubiquitin
E: Ubiquitin
F: Fanconi anemia-associated protein of 20 kDa
G: Ubiquitin
H: Ubiquitin
I: Fanconi anemia-associated protein of 20 kDa
J: Ubiquitin
K: Ubiquitin
L: Fanconi anemia-associated protein of 20 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,84716
Polymers88,58512
Non-polymers2624
Water6,233346
1
A: Ubiquitin
C: Fanconi anemia-associated protein of 20 kDa
H: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2124
Polymers22,1463
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-12 kcal/mol
Surface area10160 Å2
MethodPISA
2
B: Ubiquitin
G: Ubiquitin
I: Fanconi anemia-associated protein of 20 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2124
Polymers22,1463
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-12 kcal/mol
Surface area10230 Å2
MethodPISA
3
D: Ubiquitin
F: Fanconi anemia-associated protein of 20 kDa
K: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2124
Polymers22,1463
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-11 kcal/mol
Surface area10190 Å2
MethodPISA
4
E: Ubiquitin
J: Ubiquitin
L: Fanconi anemia-associated protein of 20 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2124
Polymers22,1463
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-11 kcal/mol
Surface area10130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.767, 45.850, 172.900
Angle α, β, γ (deg.)90.00, 98.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22D
13A
23E
14A
24G
15A
25H
16A
26J
17A
27K
18B
28D
19B
29E
110B
210G
111B
211H
112B
212J
113B
213K
114C
214F
115C
215I
116C
216L
117D
217E
118D
218G
119D
219H
120D
220J
121D
221K
122E
222G
123E
223H
124E
224J
125E
225K
126F
226I
127F
227L
128G
228H
129G
229J
130G
230K
131H
231J
132H
232K
133I
233L
134J
234K

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYAA1 - 761 - 76
21METMETGLYGLYBB1 - 761 - 76
12METMETGLYGLYAA1 - 761 - 76
22METMETGLYGLYDD1 - 761 - 76
13METMETGLYGLYAA1 - 761 - 76
23METMETGLYGLYEE1 - 761 - 76
14METMETGLYGLYAA1 - 761 - 76
24METMETGLYGLYGG1 - 761 - 76
15METMETARGARGAA1 - 741 - 74
25METMETARGARGHH1 - 741 - 74
16METMETGLYGLYAA1 - 761 - 76
26METMETGLYGLYJJ1 - 761 - 76
17METMETGLYGLYAA1 - 761 - 76
27METMETGLYGLYKK1 - 761 - 76
18METMETGLYGLYBB1 - 761 - 76
28METMETGLYGLYDD1 - 761 - 76
19METMETGLYGLYBB1 - 761 - 76
29METMETGLYGLYEE1 - 761 - 76
110METMETGLYGLYBB1 - 761 - 76
210METMETGLYGLYGG1 - 761 - 76
111METMETARGARGBB1 - 741 - 74
211METMETARGARGHH1 - 741 - 74
112METMETGLYGLYBB1 - 761 - 76
212METMETGLYGLYJJ1 - 761 - 76
113METMETGLYGLYBB1 - 761 - 76
213METMETGLYGLYKK1 - 761 - 76
114ALAALATHRTHRCC143 - 1797 - 43
214ALAALATHRTHRFF143 - 1797 - 43
115ALAALATRPTRPCC143 - 1807 - 44
215ALAALATRPTRPII143 - 1807 - 44
116LEULEUTHRTHRCC144 - 1798 - 43
216LEULEUTHRTHRLL144 - 1798 - 43
117METMETGLYGLYDD1 - 761 - 76
217METMETGLYGLYEE1 - 761 - 76
118METMETGLYGLYDD1 - 761 - 76
218METMETGLYGLYGG1 - 761 - 76
119METMETARGARGDD1 - 741 - 74
219METMETARGARGHH1 - 741 - 74
120METMETGLYGLYDD1 - 761 - 76
220METMETGLYGLYJJ1 - 761 - 76
121METMETGLYGLYDD1 - 761 - 76
221METMETGLYGLYKK1 - 761 - 76
122METMETGLYGLYEE1 - 761 - 76
222METMETGLYGLYGG1 - 761 - 76
123METMETARGARGEE1 - 741 - 74
223METMETARGARGHH1 - 741 - 74
124METMETGLYGLYEE1 - 761 - 76
224METMETGLYGLYJJ1 - 761 - 76
125METMETGLYGLYEE1 - 761 - 76
225METMETGLYGLYKK1 - 761 - 76
126ALAALATHRTHRFF143 - 1797 - 43
226ALAALATHRTHRII143 - 1797 - 43
127LEULEUTHRTHRFF144 - 1798 - 43
227LEULEUTHRTHRLL144 - 1798 - 43
128METMETARGARGGG1 - 741 - 74
228METMETARGARGHH1 - 741 - 74
129METMETGLYGLYGG1 - 761 - 76
229METMETGLYGLYJJ1 - 761 - 76
130METMETGLYGLYGG1 - 761 - 76
230METMETGLYGLYKK1 - 761 - 76
131METMETARGARGHH1 - 741 - 74
231METMETARGARGJJ1 - 741 - 74
132METMETARGARGHH1 - 741 - 74
232METMETARGARGKK1 - 741 - 74
133LEULEUTHRTHRII144 - 1798 - 43
233LEULEUTHRTHRLL144 - 1798 - 43
134METMETGLYGLYJJ1 - 761 - 76
234METMETGLYGLYKK1 - 761 - 76

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34

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Components

#1: Protein
Ubiquitin /


Mass: 8604.845 Da / Num. of mol.: 4 / Mutation: K63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ubc / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P0CG50
#2: Protein
Ubiquitin /


Mass: 8691.918 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ubc / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P0CG50
#3: Protein/peptide
Fanconi anemia-associated protein of 20 kDa


Mass: 4849.503 Da / Num. of mol.: 4 / Fragment: UBZ domain, UNP residues 142-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1orf86, FAAP20, FP7162 / Plasmid: pCold-GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q6NZ36
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS RESIDUE IS ADDITION MUTATION.

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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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8M DL-malic acid, 0.1M glycine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 74073 / Num. obs: 74073 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.064 / Net I/σ(I): 27
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 4.26 / % possible all: 88.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UBQ

1ubq


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.44 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23458 3529 5 %RANDOM
Rwork0.20825 ---
obs0.20957 66608 94.95 %-
all-74073 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.269 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å2-0.27 Å2
2---0.49 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6004 0 4 346 6354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196098
X-RAY DIFFRACTIONr_bond_other_d0.0070.026074
X-RAY DIFFRACTIONr_angle_refined_deg1.861.9918217
X-RAY DIFFRACTIONr_angle_other_deg1.9873.00214013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85325.235277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.862151197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.541544
X-RAY DIFFRACTIONr_chiral_restr0.0940.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216750
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021250
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_it1.6091.8633026
X-RAY DIFFRACTIONr_mcbond_other1.6081.8623025
X-RAY DIFFRACTIONr_mcangle_it2.5122.7783762
X-RAY DIFFRACTIONr_mcangle_other2.5122.7793763
X-RAY DIFFRACTIONr_scbond_it2.5382.2193072
X-RAY DIFFRACTIONr_scbond_other2.5382.2193072
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9553.1994454
X-RAY DIFFRACTIONr_long_range_B_refined7.46415.4946706
X-RAY DIFFRACTIONr_long_range_B_other7.45615.2536628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A42880.19
12B42880.19
21A44970.16
22D44970.16
31A43880.18
32E43880.18
41A45660.16
42G45660.16
51A43700.18
52H43700.18
61A45860.15
62J45860.15
71A42980.18
72K42980.18
81B43240.18
82D43240.18
91B44820.16
92E44820.16
101B43440.18
102G43440.18
111B43700.16
112H43700.16
121B43850.17
122J43850.17
131B47400.14
132K47400.14
141C17570.17
142F17570.17
151C18100.15
152I18100.15
161C17250.17
162L17250.17
171D44710.17
172E44710.17
181D47250.13
182G47250.13
191D42720.17
192H42720.17
201D46990.13
202J46990.13
211D43390.18
212K43390.18
221E44230.18
222G44230.18
231E44950.15
232H44950.15
241E45300.16
242J45300.16
251E44720.16
252K44720.16
261F16950.16
262I16950.16
271F16870.17
272L16870.17
281G42430.17
282H42430.17
291G46520.15
292J46520.15
301G43040.19
302K43040.19
311H43010.17
312J43010.17
321H43160.17
322K43160.17
331I16270.18
332L16270.18
341J43730.18
342K43730.18
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 246 -
Rwork0.314 4502 -
obs--88.45 %
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)
11.1857-0.0030.26270.8462-0.41632.2127-0.01740.04850.0610.0831-0.0093-0.01370.1122-0.12170.02670.12080.0033-0.01510.27560.04350.193310.2633-3.094115.0468
20.1017-0.0350.37082.0754-1.1732.6652-0.0618-0.04530.0282-0.19030.25470.04280.0736-0.0671-0.1930.20370.0114-0.06940.1940.01130.22829.535110.256452.1527
32.42550.2858-1.08891.56661.83923.07170.26940.18740.0688-0.0281-0.13-0.1353-0.1562-0.2088-0.13940.13520.0463-0.00440.28150.07680.193526.0196-1.98698.5184
40.8834-0.3784-0.95440.68020.80272.3786-0.11880.04690.01490.12640.14270.00240.11870.1781-0.02390.1417-0.00180.0020.2438-0.05280.2203-11.8491-14.868112.578
51.50320.36810.41521.83712.18232.8297-0.0385-0.01010.13720.08050.15060.08830.34850.4088-0.1120.28690.2064-0.18260.1829-0.14520.1629-10.5852-4.483354.2688
61.0334-0.18650.21930.2932-0.32635.9482-0.08940.1269-0.23970.09070.11140.07070.0301-0.0585-0.0220.1531-0.02340.05270.2282-0.03290.2299-28.4693-19.184213.1172
71.38770.4-0.1840.2987-0.49122.7415-0.0508-0.15260.0386-0.03470.06830.1830.0171-0.0763-0.01750.14160.04930.01390.21580.08090.300124.45894.153377.653
80.6583-0.03210.54071.2909-1.58562.87370.10750.02680.02080.08940.0393-0.00430.036-0.1042-0.14680.18480.0058-0.03390.20450.04430.194122.9358-10.642737.4537
92.9030.4391-0.08831.55060.98430.6922-0.1569-0.5048-0.1501-0.00870.04570.07950.070.11940.11130.19830.13390.02830.35580.02740.131941.49113.323879.3178
103.08740.07121.09180.97170.96671.3151-0.00310.12260.35990.02150.0392-0.08210.03560.1619-0.03610.0186-0.0045-0.03430.3325-0.10070.30931.396515.164367.4906
110.9064-1.7281-0.89713.91182.12251.42370.0488-0.10490.1628-0.01710.3614-0.5177-0.09310.0254-0.41030.21070.00830.0380.2286-0.04250.2714-18.2514.035730.2018
122.25170.15880.29760.4869-0.45473.7790.1017-0.12740.518-0.10810.0352-0.03120.07930.151-0.13690.0872-0.0114-0.03360.2407-0.11360.3028-14.591819.604872.094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 76
2X-RAY DIFFRACTION2B1 - 76
3X-RAY DIFFRACTION3C143 - 180
4X-RAY DIFFRACTION4D1 - 76
5X-RAY DIFFRACTION5E1 - 76
6X-RAY DIFFRACTION6F142 - 180
7X-RAY DIFFRACTION7G1 - 76
8X-RAY DIFFRACTION8H1 - 75
9X-RAY DIFFRACTION9I143 - 180
10X-RAY DIFFRACTION10J1 - 76
11X-RAY DIFFRACTION11K1 - 76
12X-RAY DIFFRACTION12L144 - 180

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