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Entry
Database: PDB / ID: 7ghh
TitleGroup deposition SARS-CoV-2 main protease in complex with inhibitors from the COVID Moonshot -- Crystal Structure of SARS-CoV-2 main protease in complex with TOB-UNK-c2aba166-1 (Mpro-x3325)
Components3C-like proteinase
KeywordsVIRAL PROTEIN / Diamond Light Source / I04-1 / COVID Moonshot / CMD / Mpro / fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / mRNA (guanine-N7)-methyltransferase / omega peptidase activity / methyltransferase cap1 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / single-stranded RNA binding / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / lipid binding / DNA-templated transcription / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
1-[4-(prop-2-yn-1-yl)piperazin-1-yl]ethan-1-one / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsFearon, D. / Aimon, A. / Aschenbrenner, J.C. / Balcomb, B.H. / Bertram, F.K.R. / Brandao-Neto, J. / Dias, A. / Douangamath, A. / Dunnett, L. / Godoy, A.S. ...Fearon, D. / Aimon, A. / Aschenbrenner, J.C. / Balcomb, B.H. / Bertram, F.K.R. / Brandao-Neto, J. / Dias, A. / Douangamath, A. / Dunnett, L. / Godoy, A.S. / Gorrie-Stone, T.J. / Koekemoer, L. / Krojer, T. / Lithgo, R.M. / Lukacik, P. / Marples, P.G. / Mikolajek, H. / Nelson, E. / Owen, C.D. / Powell, A.J. / Rangel, V.L. / Skyner, R. / Strain-Damerell, C.M. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Walsh, M.A. / von Delft, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust224021/Z/21/Z United Kingdom
CitationJournal: Science / Year: 2023
Title: Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors.
Authors: Boby, M.L. / Fearon, D. / Ferla, M. / Filep, M. / Koekemoer, L. / Robinson, M.C. / Chodera, J.D. / Lee, A.A. / London, N. / von Delft, A. / von Delft, F. / Achdout, H. / Aimon, A. / Alonzi, ...Authors: Boby, M.L. / Fearon, D. / Ferla, M. / Filep, M. / Koekemoer, L. / Robinson, M.C. / Chodera, J.D. / Lee, A.A. / London, N. / von Delft, A. / von Delft, F. / Achdout, H. / Aimon, A. / Alonzi, D.S. / Arbon, R. / Aschenbrenner, J.C. / Balcomb, B.H. / Bar-David, E. / Barr, H. / Ben-Shmuel, A. / Bennett, J. / Bilenko, V.A. / Borden, B. / Boulet, P. / Bowman, G.R. / Brewitz, L. / Brun, J. / Bvnbs, S. / Calmiano, M. / Carbery, A. / Carney, D.W. / Cattermole, E. / Chang, E. / Chernyshenko, E. / Clyde, A. / Coffland, J.E. / Cohen, G. / Cole, J.C. / Contini, A. / Cox, L. / Croll, T.I. / Cvitkovic, M. / De Jonghe, S. / Dias, A. / Donckers, K. / Dotson, D.L. / Douangamath, A. / Duberstein, S. / Dudgeon, T. / Dunnett, L.E. / Eastman, P. / Erez, N. / Eyermann, C.J. / Fairhead, M. / Fate, G. / Fedorov, O. / Fernandes, R.S. / Ferrins, L. / Foster, R. / Foster, H. / Fraisse, L. / Gabizon, R. / Garcia-Sastre, A. / Gawriljuk, V.O. / Gehrtz, P. / Gileadi, C. / Giroud, C. / Glass, W.G. / Glen, R.C. / Glinert, I. / Godoy, A.S. / Gorichko, M. / Gorrie-Stone, T. / Griffen, E.J. / Haneef, A. / Hassell Hart, S. / Heer, J. / Henry, M. / Hill, M. / Horrell, S. / Huang, Q.Y.J. / Huliak, V.D. / Hurley, M.F.D. / Israely, T. / Jajack, A. / Jansen, J. / Jnoff, E. / Jochmans, D. / John, T. / Kaminow, B. / Kang, L. / Kantsadi, A.L. / Kenny, P.W. / Kiappes, J.L. / Kinakh, S.O. / Kovar, B. / Krojer, T. / La, V.N.T. / Laghnimi-Hahn, S. / Lefker, B.A. / Levy, H. / Lithgo, R.M. / Logvinenko, I.G. / Lukacik, P. / Macdonald, H.B. / MacLean, E.M. / Makower, L.L. / Malla, T.R. / Marples, P.G. / Matviiuk, T. / McCorkindale, W. / McGovern, B.L. / Melamed, S. / Melnykov, K.P. / Michurin, O. / Miesen, P. / Mikolajek, H. / Milne, B.F. / Minh, D. / Morris, A. / Morris, G.M. / Morwitzer, M.J. / Moustakas, D. / Mowbray, C.E. / Nakamura, A.M. / Neto, J.B. / Neyts, J. / Nguyen, L. / Noske, G.D. / Oleinikovas, V. / Oliva, G. / Overheul, G.J. / Owen, C.D. / Pai, R. / Pan, J. / Paran, N. / Payne, A.M. / Perry, B. / Pingle, M. / Pinjari, J. / Politi, B. / Powell, A. / Psenak, V. / Pulido, I. / Puni, R. / Rangel, V.L. / Reddi, R.N. / Rees, P. / Reid, S.P. / Reid, L. / Resnick, E. / Ripka, E.G. / Robinson, R.P. / Rodriguez-Guerra, J. / Rosales, R. / Rufa, D.A. / Saar, K. / Saikatendu, K.S. / Salah, E. / Schaller, D. / Scheen, J. / Schiffer, C.A. / Schofield, C.J. / Shafeev, M. / Shaikh, A. / Shaqra, A.M. / Shi, J. / Shurrush, K. / Singh, S. / Sittner, A. / Sjo, P. / Skyner, R. / Smalley, A. / Smeets, B. / Smilova, M.D. / Solmesky, L.J. / Spencer, J. / Strain-Damerell, C. / Swamy, V. / Tamir, H. / Taylor, J.C. / Tennant, R.E. / Thompson, W. / Thompson, A. / Tomasio, S. / Tomlinson, C.W.E. / Tsurupa, I.S. / Tumber, A. / Vakonakis, I. / van Rij, R.P. / Vangeel, L. / Varghese, F.S. / Vaschetto, M. / Vitner, E.B. / Voelz, V. / Volkamer, A. / Walsh, M.A. / Ward, W. / Weatherall, C. / Weiss, S. / White, K.M. / Wild, C.F. / Witt, K.D. / Wittmann, M. / Wright, N. / Yahalom-Ronen, Y. / Yilmaz, N.K. / Zaidmann, D. / Zhang, I. / Zidane, H. / Zitzmann, N. / Zvornicanin, S.N.
History
DepositionAug 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Author supporting evidence / Database references
Category: citation / citation_author / pdbx_entity_instance_feature
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3827
Polymers33,8261
Non-polymers5576
Water5,945330
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,76514
Polymers67,6512
Non-polymers1,11412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5070 Å2
ΔGint5 kcal/mol
Surface area25300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.811, 53.327, 44.441
Angle α, β, γ (deg.)90.00, 101.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1283-

HOH

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Components

#1: Protein 3C-like proteinase / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33825.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-Q6U / 1-[4-(prop-2-yn-1-yl)piperazin-1-yl]ethan-1-one


Mass: 166.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
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: 1.95 Å3/Da / Density % sol: 37.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 15% PEG 4K, 5% DMSO, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 1.56→55.79 Å / Num. obs: 36873 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.053 / Rrim(I) all: 0.1 / Χ2: 0.54 / Net I/σ(I): 8 / Num. measured all: 122159
Reflection shellResolution: 1.56→1.59 Å / % possible obs: 90 % / Redundancy: 2.4 % / Rmerge(I) obs: 1.385 / Num. measured all: 3966 / Num. unique obs: 1642 / CC1/2: 0.366 / Rpim(I) all: 1.016 / Rrim(I) all: 1.726 / Χ2: 0.22 / Net I/σ(I) obs: 0.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (20-MAY-2020)refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→55.79 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.102 / SU Rfree Blow DPI: 0.101 / SU Rfree Cruickshank DPI: 0.097
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 1745 4.88 %RANDOM
Rwork0.1818 ---
obs0.1839 35781 96 %-
Displacement parametersBiso mean: 28.73 Å2
Baniso -1Baniso -2Baniso -3
1--4.5633 Å20 Å2-3.9757 Å2
2--4.0805 Å20 Å2
3---0.4828 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.56→55.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 32 330 2709
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082449HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.983327HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d833SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes421HARMONIC5
X-RAY DIFFRACTIONt_it2449HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.89
X-RAY DIFFRACTIONt_other_torsion14.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion316SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2694SEMIHARMONIC4
LS refinement shellResolution: 1.56→1.57 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2996 19 2.65 %
Rwork0.2471 697 -
all0.2485 716 -
obs--71.17 %
Refinement TLS params.Method: refined / Origin x: 11.98 Å / Origin y: 0.6463 Å / Origin z: 4.4469 Å
111213212223313233
T-0.0328 Å2-0.0123 Å20.0401 Å2--0.0353 Å2-0.0037 Å2--0.0201 Å2
L0.0727 °2-0.0127 °2-0.0017 °2-0.7455 °2-0.6465 °2--0.6233 °2
S-0.0433 Å °0.0249 Å °-0.0154 Å °0.0143 Å °0.0489 Å °-0.033 Å °-0.0087 Å °-0.0233 Å °-0.0056 Å °
Refinement TLS groupSelection details: { A|* }

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