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- PDB-5bkn: Crystallographic structure of a cubic crystal form of STMV (84.5 ... -

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Basic information

Entry
Database: PDB / ID: 5bkn
TitleCrystallographic structure of a cubic crystal form of STMV (84.5 degree rotation) grown from chloride
Components
  • Coat protein
  • RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsVIRUS / anions / RNA / ion channel / fivefold vertex / crystallization
Function / homologySatellite virus coat domain superfamily / viral capsid / structural molecule activity / RNA / RNA (> 10) / Coat protein
Function and homology information
Biological speciesSatellite tobacco mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMcPherson, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structures of additional crystal forms of Satellite tobacco mosaic virus grown from a variety of salts.
Authors: McPherson, A.
History
DepositionMar 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
h: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
n: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
kk: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)404,92579
Polymers403,66339
Non-polymers1,26240
Water11,331629
1
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
h: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
n: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
kk: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules

A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
h: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
n: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
kk: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules

A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
h: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
n: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
kk: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,214,776237
Polymers1,210,990117
Non-polymers3,786120
Water2,000111
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation12_665-y+1,-z+1,x1
Unit cell
Length a, b, c (Å)234.650, 234.650, 234.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Space group name HallP223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
Components on special symmetry positions
IDModelComponents
11KK-201-

CL

21L-332-

HOH

31JJ-311-

HOH

41bb-204-

HOH

51bb-208-

HOH

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Components

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Protein , 1 types, 20 molecules ABCDEFGHIJKLMNOGGHHIIJJKK

#1: Protein
Coat protein


Mass: 17533.949 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Satellite tobacco mosaic virus / References: UniProt: P17574

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RNA chain , 10 types, 19 molecules PSaTVXYTTUUeqqhillmWWkknbb

#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2588.689 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide octamer / Source: (natural) Satellite tobacco mosaic virus
#3: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')


Mass: 1930.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide hexamer / Source: (natural) Satellite tobacco mosaic virus
#4: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2917.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide nonamer / Source: (natural) Satellite tobacco mosaic virus
#5: RNA chain
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3247.100 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide decamer / Source: (natural) Satellite tobacco mosaic virus
#6: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3629.032 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide dodecamer / Source: (natural) Satellite tobacco mosaic virus
#7: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2098.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide heptamer / Source: (natural) Satellite tobacco mosaic virus
#8: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')


Mass: 1792.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide hexamer / Source: (natural) Satellite tobacco mosaic virus
#9: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2710.535 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide nonamer / Source: (natural) Satellite tobacco mosaic virus
#10: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2404.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide octamer / Source: (natural) Satellite tobacco mosaic virus
#11: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3905.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide dodecamer / Source: (natural) Satellite tobacco mosaic virus

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Non-polymers , 3 types, 669 molecules

#12: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 629 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.88 % / Description: large octahedra
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Crystals were grown by sitting drop vapor diffusion in Cryschem plates using .6 ml reservoirs. The drops were composed of equal volumes of a 5 mg/ml virus stock solution of 0.1 M phosphate ...Details: Crystals were grown by sitting drop vapor diffusion in Cryschem plates using .6 ml reservoirs. The drops were composed of equal volumes of a 5 mg/ml virus stock solution of 0.1 M phosphate at pH 6.5, and the reservoir solution, which was 8% NaCl w/v in 0.1 M phosphate at pH 6.0. Crystallization was at 4 degrees C.

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→75 Å / Num. obs: 85962 / % possible obs: 1 % / Redundancy: 9.4 % / Biso Wilson estimate: 43.53 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.128 / Rsym value: 0.126 / Net I/σ(I): 21.2
Reflection shellResolution: 3→3.15 Å / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7300 / CC1/2: 0.967

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OQ8

4oq8


Resolution: 3→65.08 Å / SU ML: 0.3763 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2551 4512 5.27 %
Rwork0.2078 81137 -
obs0.2103 85649 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.8 Å2
Refinement stepCycle: LAST / Resolution: 3→65.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22508 2974 40 629 26151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005526752
X-RAY DIFFRACTIONf_angle_d0.823537158
X-RAY DIFFRACTIONf_chiral_restr0.05874454
X-RAY DIFFRACTIONf_plane_restr0.00684319
X-RAY DIFFRACTIONf_dihedral_angle_d12.923610266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.030.3751520.32772618X-RAY DIFFRACTION97.67
3.03-3.070.34021260.29572702X-RAY DIFFRACTION98.98
3.07-3.110.32461600.2882668X-RAY DIFFRACTION99.65
3.11-3.150.32251330.26542690X-RAY DIFFRACTION99.96
3.15-3.190.32871570.26362680X-RAY DIFFRACTION100
3.19-3.230.29561360.23842728X-RAY DIFFRACTION100
3.23-3.280.30851550.25042706X-RAY DIFFRACTION99.97
3.28-3.330.31911690.23932695X-RAY DIFFRACTION99.97
3.33-3.380.30741630.23932624X-RAY DIFFRACTION99.82
3.38-3.430.3241690.24022714X-RAY DIFFRACTION99.83
3.43-3.490.30341390.23132697X-RAY DIFFRACTION99.89
3.49-3.560.29141240.23342722X-RAY DIFFRACTION99.89
3.56-3.620.28821570.22472698X-RAY DIFFRACTION99.72
3.62-3.70.26431370.20712668X-RAY DIFFRACTION99.82
3.7-3.780.26221690.2072740X-RAY DIFFRACTION99.66
3.78-3.870.22351350.19042675X-RAY DIFFRACTION99.4
3.87-3.960.23751460.18482662X-RAY DIFFRACTION99.26
3.96-4.070.2541560.18622702X-RAY DIFFRACTION99.2
4.07-4.190.23211140.17922743X-RAY DIFFRACTION98.96
4.19-4.320.1941440.17992666X-RAY DIFFRACTION98.8
4.33-4.480.23291920.16262676X-RAY DIFFRACTION99.41
4.48-4.660.18681660.15252668X-RAY DIFFRACTION99.37
4.66-4.870.2171770.15782677X-RAY DIFFRACTION98.89
4.87-5.130.1971670.15632667X-RAY DIFFRACTION99.61
5.13-5.450.23351090.18532773X-RAY DIFFRACTION99.93
5.45-5.870.22761690.19212730X-RAY DIFFRACTION99.93
5.87-6.460.25231330.21142775X-RAY DIFFRACTION100
6.46-7.390.24511580.21132752X-RAY DIFFRACTION100
7.4-9.30.21771340.19482786X-RAY DIFFRACTION100
9.31-65.080.24251660.23672835X-RAY DIFFRACTION98.3
Refinement TLS params.Method: refined / Origin x: 89.4076366131 Å / Origin y: 175.216636296 Å / Origin z: 28.67716789 Å
111213212223313233
T0.283656331782 Å2-0.0632675932198 Å2-3.67895244569E-5 Å2-0.348031308145 Å20.0355294637125 Å2--0.10401325559 Å2
L0.214864806811 °20.0693341308798 °2-0.119754852656 °2-0.253956094684 °20.0482804939303 °2--0.242766880491 °2
S-0.0400117127796 Å °0.223253053268 Å °0.019638882457 Å °-0.201609984806 Å °0.0605837168585 Å °-0.0622211452562 Å °-0.112102835209 Å °0.0433438554644 Å °0.00951598125889 Å °
Refinement TLS groupSelection details: all

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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