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- PDB-5odq: Heterodisulfide reductase / [NiFe]-hydrogenase complex from Metha... -

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Basic information

Entry
Database: PDB / ID: 5odq
TitleHeterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus soaked with bromoethanesulfonate.
Components
  • (Heterodisulfide reductase, subunit ...) x 3
  • (Methyl-viologen reducing hydrogenase, subunit ...) x 3
KeywordsOXIDOREDUCTASE / Heterodisulfide reductase / [NiFe]-hydrogenase / FeS cluster / ferredoxin / CCG motif / methanogenesis / flavoprotein / flavin-based electron bifurcation / [2Fe-2S] cluster / macromolecular complex / anaerobic / thioredoxin / bromoethanesulfonate / metabolism
Function / homology
Function and homology information


dihydromethanophenazine:CoB-CoM heterodisulfide reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / CoB--CoM heterodisulfide reductase activity / Oxidoreductases; Acting on a sulfur group of donors / hydrogenase (acceptor) / methanogenesis / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / iron-sulfur cluster binding ...dihydromethanophenazine:CoB-CoM heterodisulfide reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / CoB--CoM heterodisulfide reductase activity / Oxidoreductases; Acting on a sulfur group of donors / hydrogenase (acceptor) / methanogenesis / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / iron-sulfur cluster binding / nickel cation binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / Nickel-dependent hydrogenases large subunit signature 2. ...F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / FAD-dependent oxidoreductase 2, FAD binding domain / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Alpha-helical ferredoxin / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / FAD binding domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Pyridine nucleotide-disulphide oxidoreductase / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Non-cubane [4Fe-4S]-cluster / 2-bromanylethanesulfonic acid / ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / : / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / Chem-PE3 / IRON/SULFUR CLUSTER / Heterodisulfide reductase, subunit C ...Non-cubane [4Fe-4S]-cluster / 2-bromanylethanesulfonic acid / ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / : / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / Chem-PE3 / IRON/SULFUR CLUSTER / Heterodisulfide reductase, subunit C / Methyl-viologen reducing hydrogenase subunit D / Methyl-viologen reducing hydrogenase subunit G / Methyl-viologen reducing hydrogenase subunit A / Heterodisulfide reductase, subunit B / CoB--CoM heterodisulfide reductase iron-sulfur subunit A
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWagner, T. / Koch, J. / Ermler, U. / Shima, S.
CitationJournal: Science / Year: 2017
Title: Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.
Authors: Wagner, T. / Koch, J. / Ermler, U. / Shima, S.
History
DepositionJul 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heterodisulfide reductase, subunit A
B: Heterodisulfide reductase, subunit B
C: Heterodisulfide reductase, subunit C
D: Methyl-viologen reducing hydrogenase, subunit D
E: Methyl-viologen reducing hydrogenase, subunit G
F: Methyl-viologen reducing hydrogenase, subunit A
G: Heterodisulfide reductase, subunit A
H: Heterodisulfide reductase, subunit B
I: Heterodisulfide reductase, subunit C
J: Methyl-viologen reducing hydrogenase, subunit D
K: Methyl-viologen reducing hydrogenase, subunit G
L: Methyl-viologen reducing hydrogenase, subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,86165
Polymers451,69812
Non-polymers15,16253
Water16,520917
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area76800 Å2
ΔGint-854 kcal/mol
Surface area125040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)366.325, 97.352, 133.276
Angle α, β, γ (deg.)90.00, 108.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Heterodisulfide reductase, subunit ... , 3 types, 6 molecules AGBHCI

#1: Protein Heterodisulfide reductase, subunit A


Mass: 71591.672 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: /
References: UniProt: A0A2D0TCB9*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#2: Protein Heterodisulfide reductase, subunit B


Mass: 32075.318 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Details: This subunit contains two pentacoordinated non cubane [4Fe-4S] cluster
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: /
References: UniProt: A0A2D0TCB4*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#3: Protein Heterodisulfide reductase, subunit C


Mass: 20483.650 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: /
References: UniProt: A0A2D0TC97*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase

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Methyl-viologen reducing hydrogenase, subunit ... , 3 types, 6 molecules DJEKFL

#4: Protein Methyl-viologen reducing hydrogenase, subunit D


Mass: 16057.495 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: /
References: UniProt: A0A2D0TC98*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#5: Protein Methyl-viologen reducing hydrogenase, subunit G


Mass: 32511.432 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: /
References: UniProt: A0A2D0TC99*PLUS, hydrogenase (acceptor)
#6: Protein Methyl-viologen reducing hydrogenase, subunit A


Mass: 53129.602 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Details: The C-terminus has been post-translationally cleaved
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: /
References: UniProt: A0A2D0TCA6*PLUS, hydrogenase (acceptor)

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Non-polymers , 12 types, 970 molecules

#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical
ChemComp-9S8 / Non-cubane [4Fe-4S]-cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#12: Chemical
ChemComp-9SB / 2-bromanylethanesulfonic acid


Mass: 189.028 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5BrO3S
#13: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#14: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#15: Chemical ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER


Mass: 195.591 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3HFeN2NiO
#16: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL / Polyethylene glycol


Mass: 634.751 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H58O15
#17: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#18: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 917 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.36 %
Description: Black thick plate square shape of about 0.2-0.4 mm length.
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: All crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution using the sitting drop method (96-well 2-drop MRC Crystallization Plates in polystyrene, ...Details: All crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution using the sitting drop method (96-well 2-drop MRC Crystallization Plates in polystyrene, Molecular Dimensions, Suffolk, UK). The crystallization reservoir contained 100 mM Tris/HCl, pH 8.5, 30% (w/v) polyethylene glycol 4000, and 200 mM Na acetate trihydrate. Crystallization drop contained 1 ul HdrABC-MvhAGD at 25 mg/ml premixed with 2 mM FAD and 1 ul of precipitant. The soaking experiment with the bromoethanesulfonate was done by soaking the crystals in the same crystallization solution supplemented with 66 mM of bromoethanesulfonate for 7 min. The crystal has been cryo-protected using the the mother liquor solution supplemented with 30% glycerol and 10 mM bromoethanesulfonate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91941 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91941 Å / Relative weight: 1
ReflectionResolution: 2.15→48.85 Å / Num. obs: 241487 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 17.13 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.086 / Net I/σ(I): 8
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 35106 / CC1/2: 0.327 / Rpim(I) all: 0.249 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ODC

5odc


Resolution: 2.15→48.68 Å / Cor.coef. Fo:Fc: 0.9051 / Cor.coef. Fo:Fc free: 0.8848 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.217 / SU Rfree Blow DPI: 0.167
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 12098 5.01 %RANDOM
Rwork0.1962 ---
obs0.1973 241485 99.98 %-
Displacement parametersBiso mean: 33.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.4394 Å20 Å2-0.7639 Å2
2--0.5899 Å20 Å2
3----1.0293 Å2
Refine analyzeLuzzati coordinate error obs: 0.291 Å
Refinement stepCycle: 1 / Resolution: 2.15→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62041 0 1541 917 64499
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00663314HARMONIC4
X-RAY DIFFRACTIONt_angle_deg0.94115087HARMONIC6
X-RAY DIFFRACTIONt_dihedral_angle_d14287SINUSOIDAL5
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes821HARMONIC5
X-RAY DIFFRACTIONt_gen_planes9032HARMONIC35
X-RAY DIFFRACTIONt_it63314HARMONIC20
X-RAY DIFFRACTIONt_nbd29SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.31
X-RAY DIFFRACTIONt_other_torsion15.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4133SEMIHARMONIC5
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_contact71798SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2859 894 5.04 %
Rwork0.2614 16855 -
all0.2626 17749 -
obs--99.98 %
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)
10.5744-0.26410.062400.0060.3912-0.08650.0060.29090.03290.0447-0.18790.086-0.10370.04170.01360.0324-0.1443-0.09660.00390.089433.44388.200465.9582
20.73650.33910.49611.10740.13530.3266-0.01160.046-0.03170.0058-0.00330.05730.0261-0.01630.01490.01690.031-0.11180.0128-0.0389-0.006220.3213-38.366817.569
30.41990.02460.1590.53240.62311.08290.00090.00810.00610.00030.0070.004-0.0093-0.004-0.00790.0680.0281-0.05390.0663-0.0043-0.109333.5329-23.547814.6432
40.8393-0.06971.38411.68530.36041.0224-0.0272-0.01430.02570.0010.0129-0.00830.04470.02790.01420.01370.0556-0.160.0016-0.06740.001849.6928-2.329287.0629
50.16040.23570.78590.10470.31611.0689-0.0312-0.04950.0539-0.0078-0.02920.10380.04550.00970.0604-0.04090.0834-0.2225-0.022-0.13140.055555.62657.9541116.616
60.17960.26490.14690.63320.37430.4384-0.0734-0.0680.10380.0139-0.07360.06630.10150.08540.147-0.08240.048-0.20360.0907-0.1437-0.018774.270814.0504132.4564
70.2693-0.02130.12580.0042-0.04210.2126-0.0447-0.0581-0.0001-0.02310.011-0.0140.0899-0.14680.03370.086-0.0061-0.09520.0389-0.01-0.055211.4565-2.688852.0702
81.3150.26070.63980.15570.03950.48140.0002-0.01330.0715-0.0150.019-0.0739-0.01540.0348-0.0192-0.04550.1154-0.13740.03550.01710.033578.7801-4.401950.6248
91.0755-0.46450.2640.2957-0.01950.1603-0.0020.0064-0.0080.00280.0006-0.01430.020.03490.00130.04710.1479-0.13320.01140.0088-0.018668.45-21.62651.9756
100.7788-0.04620.24080.7092-0.20650.7212-0.00560.0139-0.00510.02190.003-0.01260.0119-0.00440.00270.06380.0509-0.13440.01970.0036-0.05022.09525.145524.1645
110.64050.01830.50860.1646-0.03180.7905-0.0255-0.02350.05880.0645-0.00330.04350.05540.02560.02870.0641-0.0092-0.1242-0.01030.0306-0.0401-26.961914.238116.9297
120.4978-0.16360.12530.16990.05230.6867-0.02570.06310.01560.0082-0.08970.04930.1075-0.12490.11540.0467-0.0679-0.08190.0432-0.0211-0.0523-46.84649.53572.1282
130.37540.02940.16980.3009-0.01660.0833-0.09080.03740.2090.01090.0035-0.12280.03070.00530.0873-0.0210.06040.02850.0287-0.0506-0.100722.01443.671459.8476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ L|* }
13X-RAY DIFFRACTION13{ W|* }

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