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- PDB-4wz7: Crystal structure of mitochondrial NADH:ubiquinone oxidoreductase... -

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Basic information

Entry
Database: PDB / ID: 4wz7
TitleCrystal structure of mitochondrial NADH:ubiquinone oxidoreductase from Yarrowia lipolytica.
Components
  • (NADH-ubiquinone oxidoreductase chain ...) x 6
  • (unknown subunits ...) x 2
  • (unknown subunits) x 31
  • 39-kDa subunit
  • NADH dehydrogenase subunit 2
  • NUAM protein
  • NUBM protein
  • NUCM protein
  • NUGM protein
  • Subunit NUHM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
KeywordsOXIDOREDUCTASE / Complex I / respiratory chain / mitochondria
Function / homology
Function and homology information


NADH dehydrogenase / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / mitochondrial membrane ...NADH dehydrogenase / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / mitochondrial membrane / 4 iron, 4 sulfur cluster binding / mitochondrion / metal ion binding
Similarity search - Function
Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 6 / Subunit NUKM of protein NADH:Ubiquinone oxidoreductase
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.6 Å
AuthorsWirth, C. / Zickermann, V. / Brandt, U. / Hunte, C.
Funding support Germany, 4items
OrganizationGrant numberCountry
Excellence Initiative of the German Federal and State GovernmentsEXC 294 BIOSS Germany
German Research FoundationCRC 746 Germany
German Research FoundationZI 552/3-1 Germany
Excellence Initiative of the German Federal and State GovernmentsEXC 115 Germany
CitationJournal: Science / Year: 2015
Title: Structural biology. Mechanistic insight from the crystal structure of mitochondrial complex I.
Authors: Zickermann, V. / Wirth, C. / Nasiri, H. / Siegmund, K. / Schwalbe, H. / Hunte, C. / Brandt, U.
History
DepositionNov 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
1: NADH-ubiquinone oxidoreductase chain 1
2: NADH dehydrogenase subunit 2
3: NADH-ubiquinone oxidoreductase chain 3
4: NADH-ubiquinone oxidoreductase chain 4
5: NADH-ubiquinone oxidoreductase chain 5
6: NADH-ubiquinone oxidoreductase chain 6
A: NUAM protein
B: NUBM protein
C: NUCM protein
E: 39-kDa subunit
G: NUGM protein
H: Subunit NUHM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
I: Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
K: Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
L: NADH-ubiquinone oxidoreductase chain 4L
Z: unknown subunits 1
D: unknown subunits 1
F: unknown subunits 2
J: unknown subunits
M: unknown subunits
N: unknown subunits
O: unknown subunits
P: unknown subunits
Q: unknown subunits
R: unknown subunits
S: unknown subunits
T: unknown subunits
U: unknown subunits
V: unknown subunits
W: unknown subunits
X: unknown subunits
Y: unknown subunits
AA: unknown subunits
AB: unknown subunits
AC: unknown subunits
AD: unknown subunits
AE: unknown subunits
AF: unknown subunits
AG: unknown subunits
AH: unknown subunits
AI: unknown subunits
AJ: unknown subunits
AK: unknown subunits
AL: unknown subunits
AM: unknown subunits
AN: unknown subunits
AO: unknown subunits
AP: unknown subunits
AQ: unknown subunits
AR: unknown subunits
AS: unknown subunits
AT: unknown subunits
AU: unknown subunits
AV: unknown subunits
AW: unknown subunits
AX: unknown subunits
AY: unknown subunits
AZ: unknown subunits
BA: unknown subunits
BB: unknown subunits
BC: unknown subunits
BD: unknown subunits
BE: unknown subunits
BF: unknown subunits
BG: unknown subunits
BH: unknown subunits
BI: unknown subunits
hetero molecules


Theoretical massNumber of molelcules
Total (without water)656,10075
Polymers653,63867
Non-polymers2,4618
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)317.740, 317.740, 818.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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NADH-ubiquinone oxidoreductase chain ... , 6 types, 6 molecules 13456L

#1: Protein NADH-ubiquinone oxidoreductase chain 1 / Subunit ND1


Mass: 33594.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH-ubiquinone oxidoreductase chain 3 / subunit ND3


Mass: 9394.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#4: Protein NADH-ubiquinone oxidoreductase chain 4 / Subunit ND4


Mass: 46077.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#5: Protein NADH-ubiquinone oxidoreductase chain 5 / Subunit ND5


Mass: 61819.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#6: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6 / Subunit ND6


Mass: 20765.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6E9, NADH:ubiquinone reductase (H+-translocating)
#15: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L / subunit ND4L


Mass: 9815.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6D4, NADH:ubiquinone reductase (H+-translocating)

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Protein , 16 types, 17 molecules 2ABCEGHIKJOQSAKANAUBI

#2: Protein NADH dehydrogenase subunit 2 / Subunit ND2


Mass: 46159.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#7: Protein NUAM protein


Mass: 54072.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#8: Protein NUBM protein


Mass: 33143.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#9: Protein NUCM protein


Mass: 49820.746 Da / Num. of mol.: 1 / Fragment: UNP residues 23-466 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH dehydrogenase
#10: Protein 39-kDa subunit


Mass: 16613.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#11: Protein NUGM protein


Mass: 13437.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#12: Protein Subunit NUHM of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 13290.110 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#13: Protein Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 13360.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#14: Protein Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I) / PSST subunit


Mass: 20446.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT7, NADH dehydrogenase
#18: Protein unknown subunits


Mass: 5379.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#21: Protein unknown subunits


Mass: 5975.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#23: Protein unknown subunits


Mass: 4358.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#25: Protein unknown subunits


Mass: 5890.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#38: Protein unknown subunits


Mass: 6485.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#43: Protein unknown subunits


Mass: 4954.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#48: Protein unknown subunits


Mass: 77037.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)

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Unknown subunits ... , 2 types, 3 molecules ZDF

#16: Protein unknown subunits 1


Mass: 4868.993 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#17: Protein unknown subunits 2


Mass: 4613.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)

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Protein/peptide , 24 types, 41 molecules MNPRTAHUVWABAYBEXAJAVBHYARATAAAWBBBGACADAEAFAGAIAL...

#19: Protein/peptide unknown subunits


Mass: 2486.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#20: Protein/peptide unknown subunits


Mass: 4273.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#22: Protein/peptide unknown subunits


Mass: 3932.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#24: Protein/peptide unknown subunits


Mass: 2571.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#26: Protein/peptide unknown subunits


Mass: 1294.587 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#27: Protein/peptide unknown subunits


Mass: 2230.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#28: Protein/peptide unknown subunits


Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#29: Protein/peptide
unknown subunits


Mass: 783.958 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#30: Protein/peptide
unknown subunits


Mass: 1379.692 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#31: Protein/peptide unknown subunits


Mass: 1124.378 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#32: Protein/peptide
unknown subunits


Mass: 1549.902 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#33: Protein/peptide unknown subunits


Mass: 4017.944 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#34: Protein/peptide unknown subunits


Mass: 4103.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#35: Protein/peptide unknown subunits


Mass: 2996.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#36: Protein/peptide unknown subunits


Mass: 2145.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#37: Protein/peptide unknown subunits


Mass: 3081.790 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#39: Protein/peptide unknown subunits


Mass: 1464.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#40: Protein/peptide unknown subunits


Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#41: Protein/peptide unknown subunits


Mass: 954.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#42: Protein/peptide unknown subunits


Mass: 698.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#44: Protein/peptide unknown subunits


Mass: 3337.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#45: Protein/peptide unknown subunits


Mass: 3422.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#46: Protein/peptide unknown subunits


Mass: 1720.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#47: Protein/peptide unknown subunits


Mass: 1635.006 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)

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Non-polymers , 2 types, 8 molecules

#49: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#50: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.09 Å3/Da / Density % sol: 79.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: PEG 3350, calcium acetate, glycerol

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Data collection

DiffractionMean temperature: 5 K / Ambient temp details: Helium Cooling
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 183009 / % possible obs: 99 % / Redundancy: 50.6 % / Biso Wilson estimate: 82.88 Å2 / Rmerge(I) obs: 0.518 / Net I/σ(I): 8.9
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 32.6 % / Rmerge(I) obs: 5.94 / Num. unique all: 8970 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
iMOSFLMdata reduction
SHARPphasing
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.6→25 Å / Cor.coef. Fo:Fc: 0.787 / Cor.coef. Fo:Fc free: 0.7687 / SU R Cruickshank DPI: 1.9 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.505 / SU Rfree Blow DPI: 0.592 / SU Rfree Cruickshank DPI: 0.617
RfactorNum. reflection% reflectionSelection details
Rfree0.3414 2183 1.41 %RANDOM
Rwork0.3164 ---
obs0.3168 154737 84.78 %-
Displacement parametersBiso mean: 109.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.4745 Å20 Å20 Å2
2---1.4745 Å20 Å2
3---2.9489 Å2
Refine analyzeLuzzati coordinate error obs: 1.275 Å
Refinement stepCycle: LAST / Resolution: 3.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35119 0 56 0 35175
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01135419HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.548898HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9208SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes235HARMONIC2
X-RAY DIFFRACTIONt_gen_planes6041HARMONIC5
X-RAY DIFFRACTIONt_it35419HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion26.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion6103SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance30HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact41160SEMIHARMONIC4
LS refinement shellResolution: 3.6→3.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 13 1.25 %
Rwork0.176 1026 -
all0.176 1039 -
obs--84.78 %
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)
10.189-0.3948-0.55830.80050.38893.66070.0124-0.04980.06970.02160.0027-0.0472-0.05020.0509-0.0151-0.08540.09860.0577-0.05950.077-0.2349-7.1244130.0398-116.533
22.4675-0.62570.60851.4630.06210.69970.0046-0.0115-0.02510.17240.02270.00040.03310.0745-0.02740.0856-0.1275-0.2965-0.73880.0524-0.149946.303439.8152-97.778
34.98920.8584-0.3451-0.67191.07940.7265-0.0106-0.20320.190.1903-0.0101-0.1073-0.02920.0060.02070.813-0.1309-0.10570.2244-0.02380.302-2.9345131.382717.8553
4-0.74010.32-1.09431.2155-1.26242.2528-0.0281-0.2269-0.12850.28720.0230.3940.0367-0.09350.00510.1553-0.06770.0109-0.11440.00580.0229.661720.572-88.1536
50.7635-0.68230.37992.6604-0.34080.52640.0518-0.0122-0.06820.02590.0324-0.51570.23130.3208-0.08420.18050.0595-0.326-0.1640.02460.117677.928125.6762-95.5825
66.48540.7529-1.11329.56290.034310.22650.0145-0.0864-0.03340.0750.00260.0628-0.0015-0.0237-0.0170.4111-0.0040.14320.3787-0.05450.2539-53.1664127.776630.3228
7-0.02512.95050.14097.2359-2.01051.7833-0.0358-0.0351-0.12970.10160.0284-0.02650.00050.01940.00740.1756-0.04060.18550.01030.03590.0803-25.569973.0173-20.8902
80.87391.9711-0.7472.91970.07460.4933-0.0538-0.04160.04580.12670.0229-0.4310.02650.07010.03090.0914-0.164-0.0087-0.36050.1237-0.298219.346103.0402-87.0593
9-0.2815-0.4659-1.75252.4584-1.20895.142-0.0434-0.07040.02350.2575-0.01910.0863-0.0063-0.21290.06250.5919-0.2960.23720.0877-0.071-0.1677-23.3921111.2126-36.072
102.2025-2.2694-0.06171.25380.500100.03-0.0483-0.19130.0325-0.0648-0.11980.09420.08030.03480.2299-0.0613-0.00220.03980.04150.223516.5986101.5808-32.2048
114.9397-0.622.03934.1661.40653.7120.0147-0.0050.01150.011-0.0284-0.03970.00330.04520.01370.16610.068-0.15180.27970.07830.240595.3825.6937-53.1166
127.5443-0.7341-0.61386.4082-0.38155.60250.00740.0070.0485-0.06660.0065-0.115-0.04050.0431-0.01390.3101-0.0731-0.09040.06090.02360.279926.5433140.9389-40.0183
131.20730.26410.0725-0.07740.19070.0348-0.0162-0.0150.01090.02850.0043-0.25450.11070.10570.0120.0416-0.0023-0.1494-0.0850.1034-0.014476.313446.4159-88.8409
142.9833-1.59480.134-0.4417-0.356200.0195-0.0012-0.0129-0.0294-0.01030.0003-0.0180.0309-0.00920.02180.0867-0.03940.1288-0.04870.076102.311113.2573-125.383
151.26240.4912-2.03040.9216-0.329200.0588-0.0906-0.01560.0346-0.08880.04170.0705-0.13210.03-0.00920.0202-0.0103-0.09010.0054-0.1325-6.4759115.6641-110.208
16-0.26571.54413.70439.2638-1.26877.953-0.02090.0074-0.05540.0403-0.0097-0.01180.0590.00270.03060.4934-0.1281-0.02850.0574-0.00290.0542-11.93993.0823-22.5326
17-0.06271.1928-0.7993.0691.88880.96180.01530.0361-0.0102-0.0238-0.0133-0.0075-0.0065-0.0079-0.002-0.0008-0.01350.0544-0.0069-0.0280.0111-20.458794.5928-98.8024
186.63460.4203-3.67629.54652.45749.6477-0.00850.01820.0424-0.0160.02190.07540.0289-0.0867-0.01340.4458-0.03020.12770.2647-0.0660.3436-49.7596150.458829.8714
19-0.0019-0.1030.18820.36370.92080.5503-0.0170.1879-0.0214-0.10660.0248-0.05110.01290.0171-0.00780.0566-0.0621-0.1415-0.18990.0283-0.102253.89049.134-114.244
20-0.74282.03790.79964.27743.34424.32970.047-0.23040.07330.2591-0.0853-0.1287-0.1947-0.01640.03830.4499-0.13140.11340.1735-0.05690.1259-19.1217132.8993-32.0995
210.48840.10210.8427-0.0449-1.45090.3279-0.0005-0.0095-0.05340.00610.0231-0.198-0.04650.0554-0.02260.073-0.0753-0.1084-0.14010.0137-0.085848.021541.43-128.429
22-0.24370.69541.88420.8842-1.951800.0224-0.0538-0.03450.0179-0.0110.0250.0077-0.0027-0.0113-0.0487-0.0733-0.0501-0.19570.1236-0.13218.30850.0459-99.3329
230.60910.8156-0.66470.7387-1.76380-0.01880.0049-0.05060.00560.01750.04180.00170.01930.0013-0.1062-0.10650.0342-0.1719-0.0696-0.204-9.486672.9988-105.388
242.15380.4672-1.4021.9530.63441.183-0.0358-0.14120.15790.2785-0.0319-0.0257-0.1604-0.20660.06770.171-0.09610.0911-0.30670.0148-0.2355-8.4742119.568-77.4085
251.59151.92780.93027.70462.84416.36330.03110.06620.0179-0.0469-0.0646-0.08060.0241-0.00880.03350.4484-0.12990.0143-0.04860.05550.0448-3.0997131.6418-44.7085
262.0477-0.5919-0.09561.81240.07360.16180.00420.00120.09450.08040.093-0.27020.0007-0.4663-0.0973-0.0833-0.3327-0.1869-0.76430.1302-0.179619.375573.9158-93.5671
271.77890.32251.09761.5005-0.49070-0.0392-0.13870.01820.16090.0335-0.11210.12820.04330.0056-0.0032-0.08210.008-0.37660.1762-0.19917.792799.0174-85.8987
280.09520.0481-0.0910.0240.11510.53670.0135-0.0034-0.06440.0625-0.0336-0.1337-0.0293-0.03420.02010.1332-0.0472-0.0923-0.02110.02860.016854.337339.2526-61.0715
290.21660.09291.12072.9217-1.90060-0.0081-0.02810.06710.033-0.00190.00080.0153-0.02930.010.0317-0.0684-0.1309-0.12450.0557-0.003551.152185.6128-95.3964
300.6876-0.2595-0.0196-0.5179-1.07650-0.00560.0223-0.018-0.00450.0175-0.0451-0.0304-0.007-0.0119-0.0359-0.02660.0315-0.12640.03-0.072824.9377107.4206-122.261
311.2659-0.4130.6404-0.0121-0.33033.7523-0.0159-0.13090.23050.09060.0321-0.1592-0.1560.0701-0.01620.042-0.02640.0518-0.16980.1292-0.1584-0.0569105.7899-83.4659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ P|700 - P|747 U|1300 - U|1325 V|1400 - V|1421 W|1500 - W|1508 X|1600 -X|1615 Y|1700 - Y|1712 AA|1800 - AA|1817 AB|1900 - AB|1908 }
2X-RAY DIFFRACTION2{ 4|* }
3X-RAY DIFFRACTION3{ A|* }
4X-RAY DIFFRACTION4{ AN|3100 - AN|3175 AO|3200 - AO|3231 AP|3300 - AP|3310 AQ|3400 - AQ|3407 }
5X-RAY DIFFRACTION5{ 5|* }
6X-RAY DIFFRACTION6{ B|* }
7X-RAY DIFFRACTION7{ BC|4600 - BC|4619 BD|4700 - BD|4718 BE|4800 - BE|4808 BF|4900 - BF|4918 BG|5000 - BG|5017 BH|5110 - BH|5115 BI|5200 - BI|5208 }
8X-RAY DIFFRACTION8{ 6|* }
9X-RAY DIFFRACTION9{ C|* }
10X-RAY DIFFRACTION10{ AT|3700 - AT|3712 AU|3800 - AU|3857 AV|3900 - AV|3915 AW|4000 - AW|4017 AX|4100 - AX|4138 AY|4200 - AY|4208 AZ|4330 - AZ|4339 }
11X-RAY DIFFRACTION11{ AK|2800 - AK|2875 AL2900 - AL|2935 AM|3000 - AM|3016 }
12X-RAY DIFFRACTION12{ E|* }
13X-RAY DIFFRACTION13{ AC|2000 - AC|2046 AF|2300 - AF|2334 }
14X-RAY DIFFRACTION14{ AI|2600 - AI|2635 AJ|2700 - AJ|2715 }
15X-RAY DIFFRACTION15{ O|600 - O|669 }
16X-RAY DIFFRACTION16{ G|* }
17X-RAY DIFFRACTION17{ Q|900 - Q|950 }
18X-RAY DIFFRACTION18{ H|* }
19X-RAY DIFFRACTION19{ M|401 - M|429 N|500 - N|549 }
20X-RAY DIFFRACTION20{ I|* }
21X-RAY DIFFRACTION21{ R|1000 - R|1029 S|1100 - S|1168 T|1200 - T|1214 }
22X-RAY DIFFRACTION22{ J|301 - J|363 }
23X-RAY DIFFRACTION23{ D|100 - D|156Z F|200 - F|253 }
24X-RAY DIFFRACTION24{ 1|* }
25X-RAY DIFFRACTION25{ K|* }
26X-RAY DIFFRACTION26{ 2|* }
27X-RAY DIFFRACTION27{ L|* }
28X-RAY DIFFRACTION28{ AG|2400 - AG|2424 AH|2500 - AH|2514 AR|3500 - AR|3512 AS|3600 - AS|3610 BA|4400 - BA|4407 BB|4500 - BB|4517 }
29X-RAY DIFFRACTION29{ AD|2100 - AD|2146 AE|2200 - AE|2247 }
30X-RAY DIFFRACTION30{ Z|1 - Z|57 }
31X-RAY DIFFRACTION31{ 3|* }

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