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- PDB-1ben: INSULIN COMPLEXED WITH 4-HYDROXYBENZAMIDE -

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Entry
Database: PDB / ID: 1ben
TitleINSULIN COMPLEXED WITH 4-HYDROXYBENZAMIDE
Components(HUMAN INSULINInsulin (medication)) x 2
KeywordsHORMONE / INSULIN / GLUCOSE METABOLISM
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / positive regulation of cellular protein metabolic process / negative regulation of acute inflammatory response / positive regulation of dendritic spine maintenance / COPI-mediated anterograde transport / Synthesis, secretion, and deacylation of Ghrelin / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / regulation of protein localization to plasma membrane / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / Regulation of insulin secretion / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of nitric oxide mediated signal transduction / negative regulation of protein secretion / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / positive regulation of insulin receptor signaling pathway / transport vesicle / endosome lumen / neuron projection maintenance / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of cell differentiation / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of brown fat cell differentiation / regulation of synaptic plasticity / regulation of transmembrane transporter activity / positive regulation of long-term synaptic potentiation / cognition / regulation of protein localization / activation of protein kinase B activity / positive regulation of cytokine production / positive regulation of glucose import / acute-phase response / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor signaling pathway / insulin receptor binding / positive regulation of protein localization to nucleus / vasodilation / Golgi lumen / glucose metabolic process / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / wound healing / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of MAPK cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of protein kinase B signaling / positive regulation of NF-kappaB transcription factor activity / G protein-coupled receptor signaling pathway / positive regulation of cell migration / Amyloid fiber formation / Golgi membrane / regulation of transcription, DNA-templated / endoplasmic reticulum lumen / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
4-HYDROXYBENZAMIDE / Insulin
Similarity search - Component
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsSmith, G.D. / Ciszak, E. / Pangborn, W.
Citation
Journal: Protein Sci. / Year: 1996
Title: A novel complex of a phenolic derivative with insulin: structural features related to the T-->R transition.
Authors: Smith, G.D. / Ciszak, E. / Pangborn, W.
#1: Journal: Structure / Year: 1995
Title: Role of C-Terminal B-Chain Residues in Insulin Assembly: The Structure of Hexameric Lysb28Prob29-Human Insulin
Authors: Ciszak, E. / Beals, J.M. / Frank, B.H. / Baker, J.C. / Carter, N.D. / Smith, G.D.
#2: Journal: Biochemistry / Year: 1994
Title: Crystallographic Evidence for Dual Coordination Around Zinc in the T3R3 Human Insulin Hexamer
Authors: Ciszak, E. / Smith, G.D.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: The Structure of a Complex of Hexameric Insulin and 4'-Hydroxyacetanilide
Authors: Smith, G.D. / Ciszak, E.
#4: Journal: Proteins / Year: 1992
Title: The Structure of a Rhombohedral R6 Insulin/Phenol Complex
Authors: Smith, G.D. / Dodson, G.G.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984
Title: Structural Stability in the 4-Zinc Human Insulin Hexamer
Authors: Smith, G.D. / Swenson, D.C. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D.
History
DepositionFeb 15, 1996-
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN INSULIN
B: HUMAN INSULIN
C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0769
Polymers11,6354
Non-polymers4415
Water3,027168
1
A: HUMAN INSULIN
B: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8833
Polymers5,8182
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-14 kcal/mol
Surface area3680 Å2
MethodPISA
2
C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1936
Polymers5,8182
Non-polymers3754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-10 kcal/mol
Surface area3930 Å2
MethodPISA
3
A: HUMAN INSULIN
B: HUMAN INSULIN
C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,22827
Polymers34,90612
Non-polymers1,32215
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20450 Å2
ΔGint-264 kcal/mol
Surface area11720 Å2
MethodPISA
4
C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,22827
Polymers34,90612
Non-polymers1,32215
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_556-y,x-y,z+11
crystal symmetry operation3_556-x+y,-x,z+11
Buried area13770 Å2
ΔGint-245 kcal/mol
Surface area18410 Å2
MethodPISA
5
D: HUMAN INSULIN
hetero molecules

D: HUMAN INSULIN
hetero molecules

D: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
C: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
C: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
C: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,22827
Polymers34,90612
Non-polymers1,32215
Water21612
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_554-y,x-y,z-11
crystal symmetry operation3_554-x+y,-x,z-11
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10050 Å2
ΔGint-214 kcal/mol
Surface area22120 Å2
MethodPISA
6
A: HUMAN INSULIN
B: HUMAN INSULIN
C: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
C: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
C: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,21215
Polymers24,6049
Non-polymers6086
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7890 Å2
ΔGint-91 kcal/mol
Surface area15130 Å2
MethodPISA
7
C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,57818
Polymers17,4536
Non-polymers1,12512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6300 Å2
ΔGint-141 kcal/mol
Surface area9730 Å2
MethodPISA
8
A: HUMAN INSULIN
B: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6499
Polymers17,4536
Non-polymers1963
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6000 Å2
ΔGint-87 kcal/mol
Surface area10140 Å2
MethodPISA
9
B: HUMAN INSULIN
C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

B: HUMAN INSULIN
C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

B: HUMAN INSULIN
C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,07624
Polymers27,7559
Non-polymers1,32215
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area14940 Å2
ΔGint-220 kcal/mol
Surface area11430 Å2
MethodPISA
10
A: HUMAN INSULIN
B: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,66521
Polymers27,7559
Non-polymers91012
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13870 Å2
ΔGint-226 kcal/mol
Surface area11430 Å2
MethodPISA
11
D: HUMAN INSULIN
hetero molecules

D: HUMAN INSULIN
hetero molecules

D: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
hetero molecules

A: HUMAN INSULIN
B: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,66521
Polymers27,7559
Non-polymers91012
Water1629
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_554-y,x-y,z-11
crystal symmetry operation3_554-x+y,-x,z-11
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8160 Å2
ΔGint-209 kcal/mol
Surface area17140 Å2
MethodPISA
12
B: HUMAN INSULIN
hetero molecules

B: HUMAN INSULIN
hetero molecules

B: HUMAN INSULIN
hetero molecules

C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

C: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,07624
Polymers27,7559
Non-polymers1,32215
Water1629
TypeNameSymmetry operationNumber
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_556-y,x-y,z+11
crystal symmetry operation3_556-x+y,-x,z+11
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8210 Å2
ΔGint-196 kcal/mol
Surface area18160 Å2
MethodPISA
13
B: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

B: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules

B: HUMAN INSULIN
D: HUMAN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,51418
Polymers20,6046
Non-polymers91012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8630 Å2
ΔGint-184 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)80.720, 80.720, 37.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-31-

ZN

21D-31-

ZN

31D-32-

CL

41B-48-

HOH

51D-107-

HOH

61D-116-

HOH

DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT OF INSULIN CONSISTS OF TWO INSULIN MONOMERS EACH CONSISTING OF TWO HETEROCHAINS. THE ENTRY PRESENTS COORDINATES FOR MONOMER I (CHAIN IDENTIFIERS A AND B) AND II (CHAIN IDENTIFIERS C AND D). APPLYING THE THREE-FOLD CRYSTALLOGRAPHIC SYMMETRY AXIS YIELDS A HEXAMER AROUND THE AXIS. THERE ARE TWO ZINC IONS AND ONE CHLORIDE ION PER INSULIN HEXAMER LOCATED ON THE THREE-FOLD AXIS AND HAVE OCCUPANCIES OF 0.33. WATERS HOH 18, HOH 54, AND HOH 59 ARE LOCATED ON THE THREE-FOLD AXIS.

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide HUMAN INSULIN / Insulin (medication) / INSULIN


Mass: 2383.698 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: GIFT OF LILLY RESEARCH LABORATORIES / References: UniProt: P01308
#2: Protein/peptide HUMAN INSULIN / Insulin (medication) / INSULIN


Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: GIFT OF LILLY RESEARCH LABORATORIES / References: UniProt: P01308

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Non-polymers , 4 types, 173 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HBD / 4-HYDROXYBENZAMIDE


Mass: 137.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE CONFORMATIONS OF THE TWO MONOMERS ARE DIFFERENT AS THE RESULT OF A DIFFERENCE IN CONFORMATION ...THE CONFORMATIONS OF THE TWO MONOMERS ARE DIFFERENT AS THE RESULT OF A DIFFERENCE IN CONFORMATION AT THE N-TERMINI OF THE B AND D CHAINS. IN MONOMER I, B 1 - B 8 ADOPT AN EXTENDED CONFORMATION (T STATE) WHILE IN MONOMER II RESIDUES D 4 THROUGH D 8 ARE ALPHA-HELICAL (RF STATE).
Nonpolymer detailsTHE MODEL ALSO CONTAINS TWO ZINC IONS. THE FIRST ZINC ION (ZN B 31) IS COORDINATED BY THREE ...THE MODEL ALSO CONTAINS TWO ZINC IONS. THE FIRST ZINC ION (ZN B 31) IS COORDINATED BY THREE SYMMETRY RELATED HIS B 10 SIDE CHAINS AND THE SECOND (ZN D 31) BY THREE SYMMETRY RELATED HIS D 10 SIDE CHAINS. THE COORDINATION SPHERE OF ZN B 31 IS OCTAHEDRAL WITH THE REMAINING THREE SITES FILLED BY WATER, HOH 1. THE COORDINATION OF ZN D 31 IS TETRAHEDRAL TO CL D 32.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 33 %
Description: DATA WERE MEASURED FROM SIX CRYSTALS, GROWN IN MICROGRAVITY ON SHUTTLE FLIGHT, STS-60. THE R-AXIS-IIC SOFTWARE WAS USED TO INTEGRATE EACH IMAGE PLATE; SCALING AND MERGING WAS ...Description: DATA WERE MEASURED FROM SIX CRYSTALS, GROWN IN MICROGRAVITY ON SHUTTLE FLIGHT, STS-60. THE R-AXIS-IIC SOFTWARE WAS USED TO INTEGRATE EACH IMAGE PLATE; SCALING AND MERGING WAS ACCOMPLISHED WITH THE DREAM PROGRAM PACKAGE (R.H. BLESSING, CRYSTALLOGR. REV. 1, 3-58 (1987).
Crystal growMethod: slow cooling / pH: 5.7
Details: 0.05M SODIUM CITRATE, 0.007M ZINC ACETATE, 0.06M 4-HYDROXYBENZAMIDE, 1.0M SODIUM CHLORIDE, PH=5.7. CRYSTALS GROWN BY SLOW COOLING., slow cooling
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.9 mMinsulin11
20.05 Msodium citrate11
30.007 Mzinc acetate11
40.06 M4-hydroxybenzamide11
51.0 M11NaCl

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 14, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→80 Å / Num. obs: 18002 / % possible obs: 76.6 % / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Rmerge(I) obs: 0.066
Reflection
*PLUS
Num. measured all: 159339

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.4→8 Å / σ(F): 2 /
Num. reflection% reflection
obs13694 76.5 %
Displacement parametersBiso mean: 27.4 Å2
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms807 0 23 227 1057
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0140.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.942
X-RAY DIFFRACTIONp_mcangle_it3.143
X-RAY DIFFRACTIONp_scbond_it2.022
X-RAY DIFFRACTIONp_scangle_it3.373
X-RAY DIFFRACTIONp_plane_restr0.0150.025
X-RAY DIFFRACTIONp_chiral_restr0.1260.15
X-RAY DIFFRACTIONp_singtor_nbd0.1830.5
X-RAY DIFFRACTIONp_multtor_nbd0.2250.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2490.5
X-RAY DIFFRACTIONp_planar_tor3.33.5
X-RAY DIFFRACTIONp_staggered_tor14.720
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor1525
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
σ(I): 17907 / Rfactor all: 0.176 / Rfactor obs: 0.154 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS

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