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- PDB-1gav: BACTERIOPHAGE GA PROTEIN CAPSID -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1gav
TitleBACTERIOPHAGE GA PROTEIN CAPSID
ComponentsBACTERIOPHAGE GA PROTEIN CAPSID
KeywordsVIRUS / BACTERIOPHAGE / CAPSID / COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding
Similarity search - Function
MS2 Viral Coat Protein / MS2 Viral Coat Protein / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage GA (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsTars, K. / Bundule, M. / Liljas, L.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: The crystal structure of bacteriophage GA and a comparison of bacteriophages belonging to the major groups of Escherichia coli leviviruses.
Authors: Tars, K. / Bundule, M. / Fridborg, K. / Liljas, L.
History
DepositionJan 28, 1997Processing site: BNL
Revision 1.0Sep 4, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BACTERIOPHAGE GA PROTEIN CAPSID
B: BACTERIOPHAGE GA PROTEIN CAPSID
C: BACTERIOPHAGE GA PROTEIN CAPSID
D: BACTERIOPHAGE GA PROTEIN CAPSID
E: BACTERIOPHAGE GA PROTEIN CAPSID
F: BACTERIOPHAGE GA PROTEIN CAPSID
G: BACTERIOPHAGE GA PROTEIN CAPSID
H: BACTERIOPHAGE GA PROTEIN CAPSID
I: BACTERIOPHAGE GA PROTEIN CAPSID
J: BACTERIOPHAGE GA PROTEIN CAPSID
K: BACTERIOPHAGE GA PROTEIN CAPSID
L: BACTERIOPHAGE GA PROTEIN CAPSID
M: BACTERIOPHAGE GA PROTEIN CAPSID
N: BACTERIOPHAGE GA PROTEIN CAPSID
O: BACTERIOPHAGE GA PROTEIN CAPSID
P: BACTERIOPHAGE GA PROTEIN CAPSID
Q: BACTERIOPHAGE GA PROTEIN CAPSID
R: BACTERIOPHAGE GA PROTEIN CAPSID
S: BACTERIOPHAGE GA PROTEIN CAPSID
T: BACTERIOPHAGE GA PROTEIN CAPSID
U: BACTERIOPHAGE GA PROTEIN CAPSID
V: BACTERIOPHAGE GA PROTEIN CAPSID
W: BACTERIOPHAGE GA PROTEIN CAPSID
X: BACTERIOPHAGE GA PROTEIN CAPSID
Y: BACTERIOPHAGE GA PROTEIN CAPSID
Z: BACTERIOPHAGE GA PROTEIN CAPSID
1: BACTERIOPHAGE GA PROTEIN CAPSID
2: BACTERIOPHAGE GA PROTEIN CAPSID
3: BACTERIOPHAGE GA PROTEIN CAPSID
4: BACTERIOPHAGE GA PROTEIN CAPSID
5: BACTERIOPHAGE GA PROTEIN CAPSID
6: BACTERIOPHAGE GA PROTEIN CAPSID
7: BACTERIOPHAGE GA PROTEIN CAPSID
8: BACTERIOPHAGE GA PROTEIN CAPSID
9: BACTERIOPHAGE GA PROTEIN CAPSID
0: BACTERIOPHAGE GA PROTEIN CAPSID
a: BACTERIOPHAGE GA PROTEIN CAPSID
b: BACTERIOPHAGE GA PROTEIN CAPSID
c: BACTERIOPHAGE GA PROTEIN CAPSID
d: BACTERIOPHAGE GA PROTEIN CAPSID
e: BACTERIOPHAGE GA PROTEIN CAPSID
f: BACTERIOPHAGE GA PROTEIN CAPSID
g: BACTERIOPHAGE GA PROTEIN CAPSID
h: BACTERIOPHAGE GA PROTEIN CAPSID
i: BACTERIOPHAGE GA PROTEIN CAPSID


Theoretical massNumber of molelcules
Total (without water)613,59245
Polymers613,59245
Non-polymers00
Water00
1
A: BACTERIOPHAGE GA PROTEIN CAPSID
B: BACTERIOPHAGE GA PROTEIN CAPSID
C: BACTERIOPHAGE GA PROTEIN CAPSID
D: BACTERIOPHAGE GA PROTEIN CAPSID
E: BACTERIOPHAGE GA PROTEIN CAPSID
F: BACTERIOPHAGE GA PROTEIN CAPSID
G: BACTERIOPHAGE GA PROTEIN CAPSID
H: BACTERIOPHAGE GA PROTEIN CAPSID
I: BACTERIOPHAGE GA PROTEIN CAPSID
J: BACTERIOPHAGE GA PROTEIN CAPSID
K: BACTERIOPHAGE GA PROTEIN CAPSID
L: BACTERIOPHAGE GA PROTEIN CAPSID
M: BACTERIOPHAGE GA PROTEIN CAPSID
N: BACTERIOPHAGE GA PROTEIN CAPSID
O: BACTERIOPHAGE GA PROTEIN CAPSID
P: BACTERIOPHAGE GA PROTEIN CAPSID
Q: BACTERIOPHAGE GA PROTEIN CAPSID
R: BACTERIOPHAGE GA PROTEIN CAPSID
S: BACTERIOPHAGE GA PROTEIN CAPSID
T: BACTERIOPHAGE GA PROTEIN CAPSID
U: BACTERIOPHAGE GA PROTEIN CAPSID
V: BACTERIOPHAGE GA PROTEIN CAPSID
W: BACTERIOPHAGE GA PROTEIN CAPSID
X: BACTERIOPHAGE GA PROTEIN CAPSID
Y: BACTERIOPHAGE GA PROTEIN CAPSID
Z: BACTERIOPHAGE GA PROTEIN CAPSID
1: BACTERIOPHAGE GA PROTEIN CAPSID
2: BACTERIOPHAGE GA PROTEIN CAPSID
3: BACTERIOPHAGE GA PROTEIN CAPSID
4: BACTERIOPHAGE GA PROTEIN CAPSID
5: BACTERIOPHAGE GA PROTEIN CAPSID
6: BACTERIOPHAGE GA PROTEIN CAPSID
7: BACTERIOPHAGE GA PROTEIN CAPSID
8: BACTERIOPHAGE GA PROTEIN CAPSID
9: BACTERIOPHAGE GA PROTEIN CAPSID
0: BACTERIOPHAGE GA PROTEIN CAPSID
a: BACTERIOPHAGE GA PROTEIN CAPSID
b: BACTERIOPHAGE GA PROTEIN CAPSID
c: BACTERIOPHAGE GA PROTEIN CAPSID
d: BACTERIOPHAGE GA PROTEIN CAPSID
e: BACTERIOPHAGE GA PROTEIN CAPSID
f: BACTERIOPHAGE GA PROTEIN CAPSID
g: BACTERIOPHAGE GA PROTEIN CAPSID
h: BACTERIOPHAGE GA PROTEIN CAPSID
i: BACTERIOPHAGE GA PROTEIN CAPSID

A: BACTERIOPHAGE GA PROTEIN CAPSID
B: BACTERIOPHAGE GA PROTEIN CAPSID
C: BACTERIOPHAGE GA PROTEIN CAPSID
D: BACTERIOPHAGE GA PROTEIN CAPSID
E: BACTERIOPHAGE GA PROTEIN CAPSID
F: BACTERIOPHAGE GA PROTEIN CAPSID
G: BACTERIOPHAGE GA PROTEIN CAPSID
H: BACTERIOPHAGE GA PROTEIN CAPSID
I: BACTERIOPHAGE GA PROTEIN CAPSID
J: BACTERIOPHAGE GA PROTEIN CAPSID
K: BACTERIOPHAGE GA PROTEIN CAPSID
L: BACTERIOPHAGE GA PROTEIN CAPSID
M: BACTERIOPHAGE GA PROTEIN CAPSID
N: BACTERIOPHAGE GA PROTEIN CAPSID
O: BACTERIOPHAGE GA PROTEIN CAPSID
P: BACTERIOPHAGE GA PROTEIN CAPSID
Q: BACTERIOPHAGE GA PROTEIN CAPSID
R: BACTERIOPHAGE GA PROTEIN CAPSID
S: BACTERIOPHAGE GA PROTEIN CAPSID
T: BACTERIOPHAGE GA PROTEIN CAPSID
U: BACTERIOPHAGE GA PROTEIN CAPSID
V: BACTERIOPHAGE GA PROTEIN CAPSID
W: BACTERIOPHAGE GA PROTEIN CAPSID
X: BACTERIOPHAGE GA PROTEIN CAPSID
Y: BACTERIOPHAGE GA PROTEIN CAPSID
Z: BACTERIOPHAGE GA PROTEIN CAPSID
1: BACTERIOPHAGE GA PROTEIN CAPSID
2: BACTERIOPHAGE GA PROTEIN CAPSID
3: BACTERIOPHAGE GA PROTEIN CAPSID
4: BACTERIOPHAGE GA PROTEIN CAPSID
5: BACTERIOPHAGE GA PROTEIN CAPSID
6: BACTERIOPHAGE GA PROTEIN CAPSID
7: BACTERIOPHAGE GA PROTEIN CAPSID
8: BACTERIOPHAGE GA PROTEIN CAPSID
9: BACTERIOPHAGE GA PROTEIN CAPSID
0: BACTERIOPHAGE GA PROTEIN CAPSID
a: BACTERIOPHAGE GA PROTEIN CAPSID
b: BACTERIOPHAGE GA PROTEIN CAPSID
c: BACTERIOPHAGE GA PROTEIN CAPSID
d: BACTERIOPHAGE GA PROTEIN CAPSID
e: BACTERIOPHAGE GA PROTEIN CAPSID
f: BACTERIOPHAGE GA PROTEIN CAPSID
g: BACTERIOPHAGE GA PROTEIN CAPSID
h: BACTERIOPHAGE GA PROTEIN CAPSID
i: BACTERIOPHAGE GA PROTEIN CAPSID

A: BACTERIOPHAGE GA PROTEIN CAPSID
B: BACTERIOPHAGE GA PROTEIN CAPSID
C: BACTERIOPHAGE GA PROTEIN CAPSID
D: BACTERIOPHAGE GA PROTEIN CAPSID
E: BACTERIOPHAGE GA PROTEIN CAPSID
F: BACTERIOPHAGE GA PROTEIN CAPSID
G: BACTERIOPHAGE GA PROTEIN CAPSID
H: BACTERIOPHAGE GA PROTEIN CAPSID
I: BACTERIOPHAGE GA PROTEIN CAPSID
J: BACTERIOPHAGE GA PROTEIN CAPSID
K: BACTERIOPHAGE GA PROTEIN CAPSID
L: BACTERIOPHAGE GA PROTEIN CAPSID
M: BACTERIOPHAGE GA PROTEIN CAPSID
N: BACTERIOPHAGE GA PROTEIN CAPSID
O: BACTERIOPHAGE GA PROTEIN CAPSID
P: BACTERIOPHAGE GA PROTEIN CAPSID
Q: BACTERIOPHAGE GA PROTEIN CAPSID
R: BACTERIOPHAGE GA PROTEIN CAPSID
S: BACTERIOPHAGE GA PROTEIN CAPSID
T: BACTERIOPHAGE GA PROTEIN CAPSID
U: BACTERIOPHAGE GA PROTEIN CAPSID
V: BACTERIOPHAGE GA PROTEIN CAPSID
W: BACTERIOPHAGE GA PROTEIN CAPSID
X: BACTERIOPHAGE GA PROTEIN CAPSID
Y: BACTERIOPHAGE GA PROTEIN CAPSID
Z: BACTERIOPHAGE GA PROTEIN CAPSID
1: BACTERIOPHAGE GA PROTEIN CAPSID
2: BACTERIOPHAGE GA PROTEIN CAPSID
3: BACTERIOPHAGE GA PROTEIN CAPSID
4: BACTERIOPHAGE GA PROTEIN CAPSID
5: BACTERIOPHAGE GA PROTEIN CAPSID
6: BACTERIOPHAGE GA PROTEIN CAPSID
7: BACTERIOPHAGE GA PROTEIN CAPSID
8: BACTERIOPHAGE GA PROTEIN CAPSID
9: BACTERIOPHAGE GA PROTEIN CAPSID
0: BACTERIOPHAGE GA PROTEIN CAPSID
a: BACTERIOPHAGE GA PROTEIN CAPSID
b: BACTERIOPHAGE GA PROTEIN CAPSID
c: BACTERIOPHAGE GA PROTEIN CAPSID
d: BACTERIOPHAGE GA PROTEIN CAPSID
e: BACTERIOPHAGE GA PROTEIN CAPSID
f: BACTERIOPHAGE GA PROTEIN CAPSID
g: BACTERIOPHAGE GA PROTEIN CAPSID
h: BACTERIOPHAGE GA PROTEIN CAPSID
i: BACTERIOPHAGE GA PROTEIN CAPSID

A: BACTERIOPHAGE GA PROTEIN CAPSID
B: BACTERIOPHAGE GA PROTEIN CAPSID
C: BACTERIOPHAGE GA PROTEIN CAPSID
D: BACTERIOPHAGE GA PROTEIN CAPSID
E: BACTERIOPHAGE GA PROTEIN CAPSID
F: BACTERIOPHAGE GA PROTEIN CAPSID
G: BACTERIOPHAGE GA PROTEIN CAPSID
H: BACTERIOPHAGE GA PROTEIN CAPSID
I: BACTERIOPHAGE GA PROTEIN CAPSID
J: BACTERIOPHAGE GA PROTEIN CAPSID
K: BACTERIOPHAGE GA PROTEIN CAPSID
L: BACTERIOPHAGE GA PROTEIN CAPSID
M: BACTERIOPHAGE GA PROTEIN CAPSID
N: BACTERIOPHAGE GA PROTEIN CAPSID
O: BACTERIOPHAGE GA PROTEIN CAPSID
P: BACTERIOPHAGE GA PROTEIN CAPSID
Q: BACTERIOPHAGE GA PROTEIN CAPSID
R: BACTERIOPHAGE GA PROTEIN CAPSID
S: BACTERIOPHAGE GA PROTEIN CAPSID
T: BACTERIOPHAGE GA PROTEIN CAPSID
U: BACTERIOPHAGE GA PROTEIN CAPSID
V: BACTERIOPHAGE GA PROTEIN CAPSID
W: BACTERIOPHAGE GA PROTEIN CAPSID
X: BACTERIOPHAGE GA PROTEIN CAPSID
Y: BACTERIOPHAGE GA PROTEIN CAPSID
Z: BACTERIOPHAGE GA PROTEIN CAPSID
1: BACTERIOPHAGE GA PROTEIN CAPSID
2: BACTERIOPHAGE GA PROTEIN CAPSID
3: BACTERIOPHAGE GA PROTEIN CAPSID
4: BACTERIOPHAGE GA PROTEIN CAPSID
5: BACTERIOPHAGE GA PROTEIN CAPSID
6: BACTERIOPHAGE GA PROTEIN CAPSID
7: BACTERIOPHAGE GA PROTEIN CAPSID
8: BACTERIOPHAGE GA PROTEIN CAPSID
9: BACTERIOPHAGE GA PROTEIN CAPSID
0: BACTERIOPHAGE GA PROTEIN CAPSID
a: BACTERIOPHAGE GA PROTEIN CAPSID
b: BACTERIOPHAGE GA PROTEIN CAPSID
c: BACTERIOPHAGE GA PROTEIN CAPSID
d: BACTERIOPHAGE GA PROTEIN CAPSID
e: BACTERIOPHAGE GA PROTEIN CAPSID
f: BACTERIOPHAGE GA PROTEIN CAPSID
g: BACTERIOPHAGE GA PROTEIN CAPSID
h: BACTERIOPHAGE GA PROTEIN CAPSID
i: BACTERIOPHAGE GA PROTEIN CAPSID


Theoretical massNumber of molelcules
Total (without water)2,454,369180
Polymers2,454,369180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area893630 Å2
ΔGint-5929 kcal/mol
Surface area758310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)272.700, 293.500, 339.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2given(0.309017, 0.809017, 0.5), (-0.809017, 0.5, -0.309017), (-0.5, -0.309017, 0.809017)
3given(1), (-1), (-1)
4given(0.5, 0.309017, 0.809017), (0.309017, 0.809017, -0.5), (-0.809017, 0.5, 0.309017)
5given(-0.309017, 0.809017, 0.5), (0.809017, 0.5, -0.309017), (-0.5, 0.309017, -0.809017)
6given(-0.5, 0.309017, 0.809017), (-0.309017, 0.809017, -0.5), (-0.809017, -0.5, -0.309017)
7given(0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017), (0.309017, -0.809017, 0.5)
8given(0.5, -0.309017, 0.809017), (-0.309017, 0.809017, 0.5), (-0.809017, -0.5, 0.309017)
9given(-0.309017, 0.809017, -0.5), (0.809017, 0.5, 0.309017), (0.5, -0.309017, -0.809017)
10given(-0.809017, 0.5, -0.309017), (0.5, 0.309017, -0.809017), (-0.309017, -0.809017, -0.5)
11given(0.309017, 0.809017, -0.5), (0.809017, -0.5, -0.309017), (-0.5, -0.309017, -0.809017)
12given(-1), (1), (-1)
13given(0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017), (-0.309017, -0.809017, 0.5)
14given(0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5), (0.809017, -0.5, 0.309017)
15given(0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017), (0.309017, -0.809017, -0.5)

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Components

#1: Protein ...
BACTERIOPHAGE GA PROTEIN CAPSID


Mass: 13635.385 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage GA (virus) / Genus: Levivirus / Species: Enterobacteria phage BZ13 / References: UniProt: P07234

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 5.53 Å3/Da / Density % sol: 77.77 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 %ammonium sulfate1drop
20.04 MTris-HCl1drop
30.15 M1dropNaCl
40.02 %1dropNaN3
50.9 M1reservoirNaCl
60.04 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 24, 1995 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 126364 / % possible obs: 68 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 4.6
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.8 / % possible all: 56
Reflection shell
*PLUS
% possible obs: 56 % / Num. unique obs: 15134

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→30 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.279 --
obs0.279 122247 66 %
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 3.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43335 0 0 0 43335
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.01
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.51.5
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it3.72
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.4→3.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.37 4435
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.01

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