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- PDB-6yft: Virus-like particle of Wenzhou levi-like virus 1 -

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Basic information

Entry
Database: PDB / ID: 6yft
TitleVirus-like particle of Wenzhou levi-like virus 1
Components
  • RNA
  • coat protein
KeywordsVIRUS LIKE PARTICLE / virus / virus-like particle / structural protein
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesWenzhou levi-like virus 1
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsRumnieks, J. / Kalnins, G. / Sisovs, M. / Lieknina, I. / Tars, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.1/16/A/104 Latvia
CitationJournal: Sci Adv / Year: 2020
Title: Three-dimensional structure of 22 uncultured ssRNA bacteriophages: Flexibility of the coat protein fold and variations in particle shapes.
Authors: Rumnieks, J. / Lieknina, I. / Kalnins, G. / Sisovs, M. / Akopjana, I. / Bogans, J. / Tars, K.
History
DepositionMar 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 16, 2022Group: Database references / Derived calculations / Category: database_2 / pdbx_struct_assembly
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.3Feb 23, 2022Group: Derived calculations / Category: pdbx_struct_assembly / Item: _pdbx_struct_assembly.details
Revision 1.4Jan 24, 2024Group: 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
AA: coat protein
AB: coat protein
AC: coat protein
AD: coat protein
AE: coat protein
AF: coat protein
AG: coat protein
AH: coat protein
AI: coat protein
AJ: coat protein
AK: coat protein
AL: coat protein
AM: coat protein
AN: coat protein
AO: coat protein
AP: coat protein
AQ: coat protein
AR: coat protein
AS: coat protein
AT: coat protein
AU: coat protein
AV: coat protein
AW: coat protein
AX: coat protein
AY: coat protein
AZ: coat protein
BA: coat protein
BB: coat protein
BC: coat protein
BD: coat protein
BE: coat protein
BF: coat protein
BG: coat protein
BH: coat protein
BI: coat protein
BJ: coat protein
BK: coat protein
BL: coat protein
BM: coat protein
BN: coat protein
BO: coat protein
BP: coat protein
BQ: coat protein
BR: coat protein
BS: coat protein
BT: coat protein
BU: coat protein
BV: coat protein
BW: coat protein
BX: coat protein
BY: coat protein
BZ: coat protein
CA: coat protein
CB: coat protein
CC: coat protein
CD: coat protein
CE: coat protein
CF: coat protein
CG: coat protein
CH: coat protein
CI: coat protein
CJ: coat protein
CK: coat protein
CL: coat protein
CM: coat protein
CN: coat protein
CO: coat protein
CP: coat protein
CQ: coat protein
CR: coat protein
CS: coat protein
CT: coat protein
CU: coat protein
CV: coat protein
CW: coat protein
CX: coat protein
CY: coat protein
CZ: coat protein
DA: coat protein
DB: coat protein
DC: coat protein
DD: coat protein
DE: coat protein
DF: coat protein
DG: coat protein
DH: coat protein
DI: coat protein
DJ: coat protein
DK: coat protein
DL: coat protein
DM: coat protein
DN: coat protein
DO: coat protein
DP: coat protein
DQ: coat protein
DR: coat protein
DS: coat protein
DT: coat protein
DU: coat protein
DV: coat protein
DW: coat protein
DX: coat protein
DY: coat protein
DZ: coat protein
EA: coat protein
EB: coat protein
EC: coat protein
ED: coat protein
EE: coat protein
EF: coat protein
EG: coat protein
EH: coat protein
EI: coat protein
EJ: coat protein
EK: coat protein
EL: coat protein
EM: coat protein
EN: coat protein
EO: coat protein
EP: coat protein
EQ: coat protein
ER: coat protein
ES: coat protein
ET: coat protein
EU: coat protein
EV: coat protein
EW: coat protein
EX: coat protein
EY: coat protein
EZ: coat protein
FA: coat protein
FB: coat protein
FC: coat protein
FD: coat protein
FE: coat protein
FF: coat protein
FG: coat protein
FH: coat protein
FI: coat protein
FJ: coat protein
FK: coat protein
FL: coat protein
FM: coat protein
FN: coat protein
FO: coat protein
FP: coat protein
FQ: coat protein
FR: coat protein
FS: coat protein
FT: coat protein
FU: coat protein
FV: coat protein
FW: coat protein
FX: coat protein
FY: coat protein
FZ: coat protein
GA: coat protein
GB: coat protein
GC: coat protein
GD: coat protein
GE: coat protein
GF: coat protein
GG: coat protein
GH: coat protein
GI: coat protein
GJ: coat protein
GK: coat protein
GL: coat protein
GM: coat protein
GN: coat protein
GO: coat protein
GP: coat protein
GQ: coat protein
GR: coat protein
GS: coat protein
GT: coat protein
GU: coat protein
GV: coat protein
GW: coat protein
GX: coat protein
GY: coat protein
GZ: coat protein
HA: coat protein
HB: coat protein
HC: coat protein
HD: coat protein
HE: coat protein
HF: coat protein
HG: coat protein
HH: coat protein
HI: coat protein
HJ: coat protein
HK: coat protein
HL: coat protein
HM: coat protein
HN: coat protein
HO: coat protein
HP: coat protein
HQ: coat protein
HR: coat protein
HS: coat protein
HT: coat protein
HU: coat protein
HV: coat protein
HW: coat protein
HX: coat protein
HY: coat protein
HZ: coat protein
IA: coat protein
IB: coat protein
IC: coat protein
ID: coat protein
IE: coat protein
IF: coat protein
IG: coat protein
IH: coat protein
II: coat protein
IJ: coat protein
IK: coat protein
IL: coat protein
IM: coat protein
IN: coat protein
IO: coat protein
IP: coat protein
IQ: coat protein
IR: coat protein
IS: coat protein
IT: coat protein
IU: coat protein
IV: coat protein
IW: coat protein
IX: coat protein
IY: coat protein
IZ: coat protein
JA: coat protein
JB: coat protein
JC: coat protein
JD: coat protein
JE: coat protein
JF: coat protein
JG: coat protein
JH: coat protein
JI: coat protein
JJ: coat protein
JK: coat protein
JL: coat protein
JM: coat protein
JN: coat protein
JO: coat protein
JP: coat protein
JQ: coat protein
JR: coat protein
JS: coat protein
JT: coat protein
JU: coat protein
JV: coat protein
JW: coat protein
JX: coat protein
JY: coat protein
JZ: coat protein
KA: coat protein
KB: coat protein
KC: coat protein
KD: coat protein
KE: coat protein
KF: coat protein
KG: coat protein
KH: coat protein
KI: coat protein
KJ: coat protein
KK: coat protein
KL: coat protein
KM: coat protein
KN: coat protein
KO: coat protein
KP: coat protein
KQ: coat protein
KR: coat protein
KS: coat protein
KT: coat protein
KU: coat protein
KV: coat protein
KW: coat protein
KX: coat protein
KY: coat protein
KZ: coat protein
LA: coat protein
LB: coat protein
LC: coat protein
LD: coat protein
LE: coat protein
LF: coat protein
LG: coat protein
LH: coat protein
LI: coat protein
LJ: coat protein
LK: coat protein
LL: coat protein
LM: coat protein
LN: coat protein
LO: coat protein
LP: coat protein
LQ: coat protein
LR: coat protein
LS: coat protein
LT: coat protein
LU: coat protein
LV: coat protein
LW: coat protein
LX: coat protein
LY: coat protein
LZ: coat protein
MA: coat protein
MB: coat protein
MC: coat protein
MD: coat protein
ME: coat protein
MF: coat protein
MG: coat protein
MH: coat protein
MI: coat protein
MJ: coat protein
MK: coat protein
ML: coat protein
MM: coat protein
MN: coat protein
MO: coat protein
MP: coat protein
MQ: coat protein
MR: coat protein
MS: coat protein
MT: coat protein
MU: coat protein
MV: coat protein
MW: coat protein
MX: coat protein
MY: coat protein
MZ: coat protein
NA: coat protein
NB: coat protein
NC: coat protein
ND: coat protein
NE: coat protein
NF: coat protein
NG: coat protein
NH: coat protein
NI: coat protein
NJ: coat protein
NK: coat protein
NL: coat protein
NM: coat protein
NN: coat protein
NO: coat protein
NP: coat protein
NQ: coat protein
NR: coat protein
NS: coat protein
NT: coat protein
NU: coat protein
NV: coat protein
RA: RNA
RB: RNA
RC: RNA
RD: RNA
RE: RNA
RF: RNA
RG: RNA
RH: RNA
RI: RNA
RJ: RNA
RK: RNA
RL: RNA
RM: RNA
RN: RNA
RO: RNA
RP: RNA
RQ: RNA
RR: RNA
RS: RNA
RT: RNA
RU: RNA
RV: RNA
RW: RNA
RX: RNA
RY: RNA
RZ: RNA
SA: RNA
SB: RNA
SC: RNA
SD: RNA
SE: RNA
SF: RNA
SG: RNA
SH: RNA
SI: RNA
SJ: RNA
SK: RNA
SL: RNA
SM: RNA
SN: RNA
SO: RNA
SP: RNA
SQ: RNA
SR: RNA
SS: RNA
ST: RNA
SU: RNA
SV: RNA
SW: RNA
SX: RNA
SY: RNA
SZ: RNA
TA: RNA
TB: RNA
TC: RNA
TD: RNA
TE: RNA
TF: RNA
TG: RNA
TH: RNA


Theoretical massNumber of molelcules
Total (without water)4,784,318420
Polymers4,784,318420
Non-polymers00
Water0
1
AA: coat protein
AB: coat protein
AC: coat protein
AD: coat protein
AE: coat protein
AF: coat protein
AG: coat protein
AH: coat protein
AI: coat protein
AJ: coat protein
AK: coat protein
AL: coat protein
AM: coat protein
AN: coat protein
AO: coat protein
AP: coat protein
AQ: coat protein
AR: coat protein
AS: coat protein
AT: coat protein
AU: coat protein
AV: coat protein
AW: coat protein
AX: coat protein
AY: coat protein
AZ: coat protein
BA: coat protein
BB: coat protein
BC: coat protein
BD: coat protein
BE: coat protein
BF: coat protein
BG: coat protein
BH: coat protein
BI: coat protein
BJ: coat protein
BK: coat protein
BL: coat protein
BM: coat protein
BN: coat protein
BO: coat protein
BP: coat protein
BQ: coat protein
BR: coat protein
BS: coat protein
BT: coat protein
BU: coat protein
BV: coat protein
BW: coat protein
BX: coat protein
BY: coat protein
BZ: coat protein
CA: coat protein
CB: coat protein
CC: coat protein
CD: coat protein
CE: coat protein
CF: coat protein
CG: coat protein
CH: coat protein
CI: coat protein
CJ: coat protein
CK: coat protein
CL: coat protein
CM: coat protein
CN: coat protein
CO: coat protein
CP: coat protein
CQ: coat protein
CR: coat protein
CS: coat protein
CT: coat protein
CU: coat protein
CV: coat protein
CW: coat protein
CX: coat protein
CY: coat protein
CZ: coat protein
DA: coat protein
DB: coat protein
DC: coat protein
DD: coat protein
DE: coat protein
DF: coat protein
DG: coat protein
DH: coat protein
DI: coat protein
DJ: coat protein
DK: coat protein
DL: coat protein
DM: coat protein
DN: coat protein
DO: coat protein
DP: coat protein
DQ: coat protein
DR: coat protein
DS: coat protein
DT: coat protein
DU: coat protein
DV: coat protein
DW: coat protein
DX: coat protein
DY: coat protein
DZ: coat protein
EA: coat protein
EB: coat protein
EC: coat protein
ED: coat protein
EE: coat protein
EF: coat protein
EG: coat protein
EH: coat protein
EI: coat protein
EJ: coat protein
EK: coat protein
EL: coat protein
EM: coat protein
EN: coat protein
EO: coat protein
EP: coat protein
EQ: coat protein
ER: coat protein
ES: coat protein
ET: coat protein
EU: coat protein
EV: coat protein
EW: coat protein
EX: coat protein
EY: coat protein
EZ: coat protein
FA: coat protein
FB: coat protein
FC: coat protein
FD: coat protein
FE: coat protein
FF: coat protein
FG: coat protein
FH: coat protein
FI: coat protein
FJ: coat protein
FK: coat protein
FL: coat protein
FM: coat protein
FN: coat protein
FO: coat protein
FP: coat protein
FQ: coat protein
FR: coat protein
FS: coat protein
FT: coat protein
FU: coat protein
FV: coat protein
FW: coat protein
FX: coat protein
FY: coat protein
FZ: coat protein
GA: coat protein
GB: coat protein
GC: coat protein
GD: coat protein
GE: coat protein
GF: coat protein
GG: coat protein
GH: coat protein
GI: coat protein
GJ: coat protein
GK: coat protein
GL: coat protein
GM: coat protein
GN: coat protein
GO: coat protein
GP: coat protein
GQ: coat protein
GR: coat protein
GS: coat protein
GT: coat protein
GU: coat protein
GV: coat protein
GW: coat protein
GX: coat protein
RA: RNA
RB: RNA
RC: RNA
RD: RNA
RE: RNA
RF: RNA
RG: RNA
RH: RNA
RI: RNA
RJ: RNA
RK: RNA
RL: RNA
RM: RNA
RN: RNA
RO: RNA
RP: RNA
RQ: RNA
RR: RNA
RS: RNA
RT: RNA
RU: RNA
RV: RNA
RW: RNA
RX: RNA
RY: RNA
RZ: RNA
SA: RNA
SB: RNA
SC: RNA
SD: RNA


Theoretical massNumber of molelcules
Total (without water)2,392,159210
Polymers2,392,159210
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodComplete virus-like particle
2
GY: coat protein
GZ: coat protein
HA: coat protein
HB: coat protein
HC: coat protein
HD: coat protein
HE: coat protein
HF: coat protein
HG: coat protein
HH: coat protein
HI: coat protein
HJ: coat protein
HK: coat protein
HL: coat protein
HM: coat protein
HN: coat protein
HO: coat protein
HP: coat protein
HQ: coat protein
HR: coat protein
HS: coat protein
HT: coat protein
HU: coat protein
HV: coat protein
HW: coat protein
HX: coat protein
HY: coat protein
HZ: coat protein
IA: coat protein
IB: coat protein
IC: coat protein
ID: coat protein
IE: coat protein
IF: coat protein
IG: coat protein
IH: coat protein
II: coat protein
IJ: coat protein
IK: coat protein
IL: coat protein
IM: coat protein
IN: coat protein
IO: coat protein
IP: coat protein
IQ: coat protein
IR: coat protein
IS: coat protein
IT: coat protein
IU: coat protein
IV: coat protein
IW: coat protein
IX: coat protein
IY: coat protein
IZ: coat protein
JA: coat protein
JB: coat protein
JC: coat protein
JD: coat protein
JE: coat protein
JF: coat protein
JG: coat protein
JH: coat protein
JI: coat protein
JJ: coat protein
JK: coat protein
JL: coat protein
JM: coat protein
JN: coat protein
JO: coat protein
JP: coat protein
JQ: coat protein
JR: coat protein
JS: coat protein
JT: coat protein
JU: coat protein
JV: coat protein
JW: coat protein
JX: coat protein
JY: coat protein
JZ: coat protein
KA: coat protein
KB: coat protein
KC: coat protein
KD: coat protein
KE: coat protein
KF: coat protein
KG: coat protein
KH: coat protein
KI: coat protein
KJ: coat protein
KK: coat protein
KL: coat protein
KM: coat protein
KN: coat protein
KO: coat protein
KP: coat protein
KQ: coat protein
KR: coat protein
KS: coat protein
KT: coat protein
KU: coat protein
KV: coat protein
KW: coat protein
KX: coat protein
KY: coat protein
KZ: coat protein
LA: coat protein
LB: coat protein
LC: coat protein
LD: coat protein
LE: coat protein
LF: coat protein
LG: coat protein
LH: coat protein
LI: coat protein
LJ: coat protein
LK: coat protein
LL: coat protein
LM: coat protein
LN: coat protein
LO: coat protein
LP: coat protein
LQ: coat protein
LR: coat protein
LS: coat protein
LT: coat protein
LU: coat protein
LV: coat protein
LW: coat protein
LX: coat protein
LY: coat protein
LZ: coat protein
MA: coat protein
MB: coat protein
MC: coat protein
MD: coat protein
ME: coat protein
MF: coat protein
MG: coat protein
MH: coat protein
MI: coat protein
MJ: coat protein
MK: coat protein
ML: coat protein
MM: coat protein
MN: coat protein
MO: coat protein
MP: coat protein
MQ: coat protein
MR: coat protein
MS: coat protein
MT: coat protein
MU: coat protein
MV: coat protein
MW: coat protein
MX: coat protein
MY: coat protein
MZ: coat protein
NA: coat protein
NB: coat protein
NC: coat protein
ND: coat protein
NE: coat protein
NF: coat protein
NG: coat protein
NH: coat protein
NI: coat protein
NJ: coat protein
NK: coat protein
NL: coat protein
NM: coat protein
NN: coat protein
NO: coat protein
NP: coat protein
NQ: coat protein
NR: coat protein
NS: coat protein
NT: coat protein
NU: coat protein
NV: coat protein
SE: RNA
SF: RNA
SG: RNA
SH: RNA
SI: RNA
SJ: RNA
SK: RNA
SL: RNA
SM: RNA
SN: RNA
SO: RNA
SP: RNA
SQ: RNA
SR: RNA
SS: RNA
ST: RNA
SU: RNA
SV: RNA
SW: RNA
SX: RNA
SY: RNA
SZ: RNA
TA: RNA
TB: RNA
TC: RNA
TD: RNA
TE: RNA
TF: RNA
TG: RNA
TH: RNA


Theoretical massNumber of molelcules
Total (without water)2,392,159210
Polymers2,392,159210
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodComplete virus-like particle
Unit cell
Length a, b, c (Å)277.471, 396.638, 399.868
Angle α, β, γ (deg.)69.660, 83.650, 83.490
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ...
coat protein


Mass: 11911.487 Da / Num. of mol.: 360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wenzhou levi-like virus 1 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: RNA chain ...
RNA /


Mass: 8269.707 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) unidentified (others)

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 10 % v/v ethanol, 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 24, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.5→61.15 Å / Num. all: 1749831 / Num. obs: 1749831 / % possible obs: 87.6 % / Redundancy: 1.8 % / Rpim(I) all: 0.307 / Rrim(I) all: 0.434 / Rsym value: 0.307 / Net I/av σ(I): 2.167 / Net I/σ(I): 2.6 / Num. measured all: 3182922
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
3.5-3.691.81.4810.52623191.4812.0951.48189.9
3.69-3.911.81.1650.62414561.1651.6471.16587.4
3.91-4.181.80.75512124230.7551.0670.75581.9
4.18-4.521.80.4071.92191490.4070.5760.40790.7
4.52-4.951.80.262.91981650.260.3680.2689.2
4.95-5.531.80.2672.91663060.2670.3770.26782.8
5.53-6.391.90.2143.61636060.2140.3030.21492.4
6.39-7.831.80.135.81302530.130.1840.1387.1
7.83-11.071.80.05612.11018690.0560.0790.05688.2
11.07-61.151.80.0384.4542850.0380.0540.03886

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Processing

Software
NameVersionClassification
MOSFLMdata collection
SCALA3.3.22data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.22data extraction
FFTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ms2

2ms2


Resolution: 3.5→61.15 Å / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.44
RfactorNum. reflection% reflection
Rfree0.2606 19893 1.14 %
Rwork0.2612 --
obs0.2612 1741933 87.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 364.17 Å2 / Biso mean: 100.6014 Å2 / Biso min: 19.4 Å2
Refinement stepCycle: final / Resolution: 3.5→61.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms302040 25200 0 0 327240
Num. residues----41880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.540.39156570.391575135817088
3.54-3.580.38036710.387579415861288
3.58-3.630.39756420.3901575675820988
3.63-3.670.38456700.3871581775884788
3.67-3.720.37736840.3838577525843688
3.72-3.770.38586690.3804578115848088
3.77-3.820.36636640.3773573105797487
3.82-3.880.36316530.3742565875724086
3.88-3.940.35276380.3645562865692486
3.94-4.010.35946300.3544545105514083
4.01-4.080.35435860.3441499175050376
4.08-4.150.33646080.3305532895389781
4.15-4.230.31487010.312601936089492
4.23-4.320.29077120.2942599396065191
4.32-4.410.26086840.2719596686035290
4.41-4.510.25926810.2621591615984290
4.51-4.620.24976950.2444587215941689
4.62-4.750.23836790.2332588795955890
4.75-4.890.22026850.2291589075959289
4.89-5.050.23916720.2402577175838988
5.05-5.230.22586410.2304558185645985
5.23-5.440.23595800.2414504125099277
5.44-5.680.22376950.2268593996009490
5.68-5.980.2197030.2185609336163693
5.98-6.360.21266950.2076602776097292
6.36-6.850.17826800.1812592435992390
6.85-7.540.15866660.1674569865765287
7.54-8.620.16526150.1668535975421281
8.62-10.860.12996840.1342607156139992
10.86-61.150.2656530.2523568155746886

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