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- PDB-4n9f: Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex -

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Basic information

Entry
Database: PDB / ID: 4n9f
TitleCrystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex
Components
  • (Transcription elongation factor B polypeptide ...) x 2
  • Core-binding factor subunit beta
  • Cullin-5
  • Virion infectivity factor
KeywordsLIGASE/VIRAL PROTEIN / Zinc Finger motif / stabilize VIf interaction with CUL5 / CUL5 / TRANSCRIPTION-VIRAL PROTEIN complex / LIGASE-VIRAL PROTEIN complex
Function / homology
Function and homology information


RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / lymphocyte differentiation ...RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / lymphocyte differentiation / ERBB2 signaling pathway / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX2 regulates genes involved in cell migration / regulation of neuron migration / RUNX2 regulates genes involved in differentiation of myeloid cells / Transcriptional regulation by RUNX2 / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / reelin-mediated signaling pathway / myeloid cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / target-directed miRNA degradation / VCB complex / elongin complex / definitive hemopoiesis / protein K11-linked ubiquitination / Regulation of RUNX1 Expression and Activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / ubiquitin ligase complex scaffold activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RUNX2 regulates osteoblast differentiation / site of DNA damage / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RUNX3 regulates p14-ARF / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / cell maturation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / viral life cycle / RNA Polymerase II Pre-transcription Events / intrinsic apoptotic signaling pathway / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / calcium channel activity / virion component / G1/S transition of mitotic cell cycle / Regulation of expression of SLITs and ROBOs / Downregulation of ERBB2 signaling / Transcriptional regulation of granulopoiesis / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / osteoblast differentiation / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / signaling receptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / Estrogen-dependent gene expression / sequence-specific DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / host cell cytoplasm / transcription coactivator activity / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / host cell plasma membrane / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
Polyomavirus Enhancer Binding Protein 2; Chain: A; / Core binding factor, beta subunit / Retroviral Vif (Viral infectivity) protein / Retroviral Vif (Viral infectivity) protein / Cullin Repeats / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / 5 helical Cullin repeat like / Cullin protein neddylation domain ...Polyomavirus Enhancer Binding Protein 2; Chain: A; / Core binding factor, beta subunit / Retroviral Vif (Viral infectivity) protein / Retroviral Vif (Viral infectivity) protein / Cullin Repeats / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / 5 helical Cullin repeat like / Cullin protein neddylation domain / Cullin, conserved site / Elongin-C / Cullin family signature. / Elongin B / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Roll / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Virion infectivity factor / Core-binding factor subunit beta / Elongin-C / Elongin-B / Virion infectivity factor / Cullin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGuo, Y.Y. / Dong, L.Y. / Huang, Z.W.
CitationJournal: Nature / Year: 2014
Title: Structural basis for hijacking CBF-b and CUL5 E3 ligase complex by HIV-1 Vif
Authors: Guo, Y.Y. / Dong, L.Y. / Qiu, X.L. / Wang, Y.S. / Zhang, B.L. / Liu, H.N. / Yu, Y. / Zang, Y. / Yang, M.J. / Huang, Z.W.
History
DepositionOct 21, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 8, 2014Provider: 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_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_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
U: Cullin-5
Y: Transcription elongation factor B polypeptide 1
X: Transcription elongation factor B polypeptide 2
a: Core-binding factor subunit beta
b: Virion infectivity factor
C: Cullin-5
E: Transcription elongation factor B polypeptide 1
D: Transcription elongation factor B polypeptide 2
F: Core-binding factor subunit beta
G: Virion infectivity factor
I: Cullin-5
K: Transcription elongation factor B polypeptide 1
J: Transcription elongation factor B polypeptide 2
L: Core-binding factor subunit beta
M: Virion infectivity factor
O: Cullin-5
Q: Transcription elongation factor B polypeptide 1
P: Transcription elongation factor B polypeptide 2
R: Core-binding factor subunit beta
S: Virion infectivity factor
V: Cullin-5
Z: Transcription elongation factor B polypeptide 1
W: Transcription elongation factor B polypeptide 2
c: Core-binding factor subunit beta
d: Virion infectivity factor
f: Cullin-5
h: Transcription elongation factor B polypeptide 1
g: Transcription elongation factor B polypeptide 2
i: Core-binding factor subunit beta
j: Virion infectivity factor
l: Cullin-5
n: Transcription elongation factor B polypeptide 1
m: Transcription elongation factor B polypeptide 2
o: Core-binding factor subunit beta
p: Virion infectivity factor
r: Cullin-5
t: Transcription elongation factor B polypeptide 1
s: Transcription elongation factor B polypeptide 2
u: Core-binding factor subunit beta
v: Virion infectivity factor
x: Cullin-5
z: Transcription elongation factor B polypeptide 1
y: Transcription elongation factor B polypeptide 2
0: Core-binding factor subunit beta
1: Virion infectivity factor
3: Cullin-5
5: Transcription elongation factor B polypeptide 1
4: Transcription elongation factor B polypeptide 2
6: Core-binding factor subunit beta
7: Virion infectivity factor
9: Cullin-5
T: Transcription elongation factor B polypeptide 1
e: Transcription elongation factor B polypeptide 2
k: Core-binding factor subunit beta
q: Virion infectivity factor
w: Cullin-5
B: Transcription elongation factor B polypeptide 1
H: Transcription elongation factor B polypeptide 2
N: Core-binding factor subunit beta
2: Virion infectivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,200,46272
Polymers1,199,67760
Non-polymers78512
Water00
1
U: Cullin-5
Y: Transcription elongation factor B polypeptide 1
X: Transcription elongation factor B polypeptide 2
a: Core-binding factor subunit beta
b: Virion infectivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0386
Polymers99,9735
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cullin-5
E: Transcription elongation factor B polypeptide 1
D: Transcription elongation factor B polypeptide 2
F: Core-binding factor subunit beta
G: Virion infectivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0386
Polymers99,9735
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Cullin-5
K: Transcription elongation factor B polypeptide 1
J: Transcription elongation factor B polypeptide 2
L: Core-binding factor subunit beta
M: Virion infectivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0386
Polymers99,9735
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
O: Cullin-5
Q: Transcription elongation factor B polypeptide 1
P: Transcription elongation factor B polypeptide 2
R: Core-binding factor subunit beta
S: Virion infectivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0386
Polymers99,9735
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
V: Cullin-5
Z: Transcription elongation factor B polypeptide 1
W: Transcription elongation factor B polypeptide 2
c: Core-binding factor subunit beta
d: Virion infectivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0386
Polymers99,9735
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
f: Cullin-5
h: Transcription elongation factor B polypeptide 1
g: Transcription elongation factor B polypeptide 2
i: Core-binding factor subunit beta
j: Virion infectivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0386
Polymers99,9735
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
l: Cullin-5
n: Transcription elongation factor B polypeptide 1
m: Transcription elongation factor B polypeptide 2
o: Core-binding factor subunit beta
p: Virion infectivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0386
Polymers99,9735
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
r: Cullin-5
t: Transcription elongation factor B polypeptide 1
s: Transcription elongation factor B polypeptide 2
u: Core-binding factor subunit beta
v: Virion infectivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0386
Polymers99,9735
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
x: Cullin-5
z: Transcription elongation factor B polypeptide 1
y: Transcription elongation factor B polypeptide 2
0: Core-binding factor subunit beta
1: Virion infectivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0386
Polymers99,9735
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
3: Cullin-5
5: Transcription elongation factor B polypeptide 1
4: Transcription elongation factor B polypeptide 2
6: Core-binding factor subunit beta
7: Virion infectivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0386
Polymers99,9735
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
9: Cullin-5
T: Transcription elongation factor B polypeptide 1
e: Transcription elongation factor B polypeptide 2
k: Core-binding factor subunit beta
q: Virion infectivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0386
Polymers99,9735
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
w: Cullin-5
B: Transcription elongation factor B polypeptide 1
H: Transcription elongation factor B polypeptide 2
N: Core-binding factor subunit beta
2: Virion infectivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0386
Polymers99,9735
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.925, 204.002, 247.866
Angle α, β, γ (deg.)65.51, 90.28, 90.50
Int Tables number1
Space group name H-MP1

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Components

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Protein , 3 types, 36 molecules UCIOVflrx39waFLRciou06kNbGMSdj...

#1: Protein
Cullin-5 / CUL-5 / Vasopressin-activated calcium-mobilizing receptor 1 / VACM-1


Mass: 36386.766 Da / Num. of mol.: 12 / Fragment: UNP residues 12-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL5, VACM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93034
#4: Protein
Core-binding factor subunit beta / CBF-beta / Polyomavirus enhancer-binding protein 2 beta subunit / PEA2-beta / PEBP2-beta / SL3-3 ...CBF-beta / Polyomavirus enhancer-binding protein 2 beta subunit / PEA2-beta / PEBP2-beta / SL3-3 enhancer factor 1 subunit beta / SL3/AKV core-binding factor beta subunit


Mass: 20272.629 Da / Num. of mol.: 12 / Fragment: UNP residues 1-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBFB, CBFbeta / Production host: Escherichia coli (E. coli) / References: UniProt: Q13951
#5: Protein
Virion infectivity factor


Mass: 20982.240 Da / Num. of mol.: 12 / Fragment: UNP residues 1-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: vif / Production host: Escherichia coli (E. coli) / References: UniProt: Q72499, UniProt: P12504*PLUS

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Transcription elongation factor B polypeptide ... , 2 types, 24 molecules YEKQZhntz5TBXDJPWgmsy4eH

#2: Protein
Transcription elongation factor B polypeptide 1 / Elongin 15 kDa subunit / Elongin-C / EloC / RNA polymerase II transcription factor SIII subunit C / SIII p15


Mass: 10843.420 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#3: Protein
Transcription elongation factor B polypeptide 2 / Elongin 18 kDa subunit / Elongin-B / EloB / RNA polymerase II transcription factor SIII subunit B / SIII p18


Mass: 11488.030 Da / Num. of mol.: 12 / Fragment: UNP residues 1-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370

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Non-polymers , 1 types, 12 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

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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: 3.99 Å3/Da / Density % sol: 69.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 281473 / % possible obs: 95.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.6 / Redundancy: 4.3 % / Net I/σ(I): 15
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.69-3.82198.6
3.82-3.97164.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JGH

4jgh


Resolution: 3.3→49.535 Å / σ(F): 1.97 / Stereochemistry target values: ML
RfactorNum. reflectionSelection details
Rfree0.3238 13494 RANDOM
Rwork0.2617 --
all0.277 278661 -
obs0.2648 266400 -
Refinement stepCycle: LAST / Resolution: 3.3→49.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms77206 0 12 0 77218
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.783
X-RAY DIFFRACTIONf_dihedral_angle_d21.084
X-RAY DIFFRACTIONf_chiral_restr0.106
X-RAY DIFFRACTIONf_plane_restr0.009
Refinement TLS params.Method: refined / Origin x: 48.2984 Å / Origin y: 5.5279 Å / Origin z: -144.855 Å
111213212223313233
T0.836 Å2-0.0058 Å2-0.0096 Å2-0.9414 Å2-0.0055 Å2--0.8797 Å2
L-0.0089 °20.0165 °20.0032 °2-0.0274 °2-0.0187 °2--0.003 °2
S0.0024 Å °0.0004 Å °0.0042 Å °0.0391 Å °-0.0105 Å °-0.0005 Å °-0.0084 Å °-0.0144 Å °0.0072 Å °
Refinement TLS groupSelection details: all

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